WorldWideScience

Sample records for pipette-held cells particles

  1. Bonded-cell model for particle fracture

    OpenAIRE

    Nguyen, Duc-Hanh; Azéma, Émilien; Sornay, Philippe; Radjaï, Farhang

    2015-01-01

    International audience; Particle degradation and fracture play an important role in natural granular flows and in many applications of granular materials. We analyze the fracture properties of two-dimensional disklike particles modeled as aggregates of rigid cells bonded along their sides by a cohesive Mohr-Coulomb law and simulated by the contact dynamics method. We show that the compressive strength scales with tensile strength between cells but depends also on the friction coefficient and ...

  2. Bonded-cell model for particle fracture.

    Science.gov (United States)

    Nguyen, Duc-Hanh; Azéma, Emilien; Sornay, Philippe; Radjai, Farhang

    2015-02-01

    Particle degradation and fracture play an important role in natural granular flows and in many applications of granular materials. We analyze the fracture properties of two-dimensional disklike particles modeled as aggregates of rigid cells bonded along their sides by a cohesive Mohr-Coulomb law and simulated by the contact dynamics method. We show that the compressive strength scales with tensile strength between cells but depends also on the friction coefficient and a parameter describing cell shape distribution. The statistical scatter of compressive strength is well described by the Weibull distribution function with a shape parameter varying from 6 to 10 depending on cell shape distribution. We show that this distribution may be understood in terms of percolating critical intercellular contacts. We propose a random-walk model of critical contacts that leads to particle size dependence of the compressive strength in good agreement with our simulation data.

  3. Particle compositions with a pre-selected cell internalization mode

    Science.gov (United States)

    Decuzzi, Paolo (Inventor); Ferrari, Mauro (Inventor)

    2012-01-01

    A method of formulating a particle composition having a pre-selected cell internalization mode involves selecting a target cell having surface receptors and obtaining particles that have i) surface moieties, that have an affinity for or are capable of binding to the surface receptors of the cell and ii) a preselected shape, where a surface distribution of the surface moieties on the particles and the shape of the particles are effective for the pre-selected cell internalization mode.

  4. Remote Control of T Cell Activation Using Magnetic Janus Particles.

    Science.gov (United States)

    Lee, Kwahun; Yi, Yi; Yu, Yan

    2016-06-20

    We report a strategy for using magnetic Janus microparticles to control the stimulation of T cell signaling with single-cell precision. To achieve this, we designed Janus particles that are magnetically responsive on one hemisphere and stimulatory to T cells on the other side. By manipulating the rotation and locomotion of Janus particles under an external magnetic field, we could control the orientation of the particle-cell recognition and thereby the initiation of T cell activation. This study demonstrates a step towards employing anisotropic material properties of Janus particles to control single-cell activities without the need of complex magnetic manipulation devices.

  5. Enhanced stopping of macro-particles in particle-in-cell simulations

    OpenAIRE

    May, J; Tonge, J; Ellis, I; Mori, W. B.; Fiuza, F.; Fonseca, R. A.; Silva,L. O.; Ren, C.

    2014-01-01

    WOS:000337107200042 (Nº de Acesso Web of Science) We derive an equation for energy transfer from relativistic charged particles to a cold background plasma appropriate for finite-size particles that are used in particle-in-cell simulation codes. Expressions for one-, two-, and three-dimensional particles are presented, with special attention given to the two-dimensional case. This energy transfer is due to the electric field of the wake set up in the background plasma by the relativistic p...

  6. Enhanced Stopping of Macro-Particles in Particle-in-Cell Simulations

    CERN Document Server

    May, Josh; Mori, Warren B; Fiúza, Frederico; Fonseca, Ricardo A; Silva, Luís O; Ren, Chuang

    2014-01-01

    We derive an equation for energy transfer from relativistic charged particles to a cold background plasma appropriate for finite-size particles that are used in particle-in-cell simulation codes. Expressions for one-, two-, and three-dimensional particles are presented, with special attention given to the two-dimensional case. This energy transfer is due to the electric field of the wake set up in the background plasma by the relativistic particle. The enhanced stopping is dependent on the $q^2/m$, where $q$ is the charge and $m$ is the mass of the relativistic particle, and therefore simulation macro-particles with large charge but identical $q/m$ will stop more rapidly. The stopping power also depends on the effective particle shape of the macro-particle. These conclusions are verified in particle-in-cell simulations. We present 2D simulations of test particles, relaxation of high-energy tails, and integrated fast ignition simulations showing that the enhanced drag on macro-particles may adversely affect th...

  7. Effects of charged particles on human tumor cells

    Directory of Open Access Journals (Sweden)

    Kathryn D Held

    2016-02-01

    Full Text Available The use of charged particle therapy in cancer treatment is growing rapidly, in large part because the exquisite dose localization of charged particles allows for higher radiation doses to be given to tumor tissue while normal tissues are exposed to lower doses and decreased volumes of normal tissues are irradiated. In addition, charged particles heavier than protons have substantial potential clinical advantages because of their additional biological effects including greater cell killing effectiveness, decreased radiation resistance of hypoxic cells in tumors and reduced cell cycle dependence of radiation response. These biological advantages depend on many factors such as endpoint, cell or tissue type, dose, dose rate or fractionation, charged particle type and energy, and oxygen concentration. This review summarizes the unique biological advantages of charged particle therapy and highlights recent research and areas of particular research needs, such as quantification of Relative Biological Effectiveness (RBE for various tumor types and radiation qualities, role of genetic background of tumor cells in determining response to charged particles, sensitivity of cancer stem-like cells to charged particles, role of charged particles in tumors with hypoxic fractions and importance of fractionation, including use of hypofractionation, with charged particles.

  8. An angular momentum conserving Affine-Particle-In-Cell method

    CERN Document Server

    Jiang, Chenfanfu; Teran, Joseph

    2016-01-01

    We present a new technique for transferring momentum and velocity between particles and grid with Particle-In-Cell (PIC) calculations which we call Affine-Particle-In-Cell (APIC). APIC represents particle velocities as locally affine, rather than locally constant as in traditional PIC. We show that this representation allows APIC to conserve linear and angular momentum across transfers while also dramatically reducing numerical diffusion usually associated with PIC. Notably, conservation is achieved with lumped mass, as opposed to the more commonly used Fluid Implicit Particle (FLIP) transfers which require a 'full' mass matrix for exact conservation. Furthermore, unlike FLIP, APIC retains a filtering property of the original PIC and thus does not accumulate velocity modes on particles as FLIP does. In particular, we demonstrate that APIC does not experience velocity instabilities that are characteristic of FLIP in a number of Material Point Method (MPM) hyperelasticity calculations. Lastly, we demonstrate th...

  9. Carbon fuel particles used in direct carbon conversion fuel cells

    Science.gov (United States)

    Cooper, John F.; Cherepy, Nerine

    2012-10-09

    A system for preparing particulate carbon fuel and using the particulate carbon fuel in a fuel cell. Carbon particles are finely divided. The finely dividing carbon particles are introduced into the fuel cell. A gas containing oxygen is introduced into the fuel cell. The finely divided carbon particles are exposed to carbonate salts, or to molten NaOH or KOH or LiOH or mixtures of NaOH or KOH or LiOH, or to mixed hydroxides, or to alkali and alkaline earth nitrates.

  10. Simulation of Cell Adhesion using a Particle Transport Model

    Science.gov (United States)

    Chesnutt, Jennifer

    2005-11-01

    An efficient computational method for simulation of cell adhesion through protein binding forces is discussed. In this method, the cells are represented by deformable elastic particles, and the protein binding is represented by a rate equation. The method is first developed for collision and adhesion of two similar cells impacting on each other from opposite directions. The computational method is then applied in a particle-transport model for a cloud of interacting and colliding cells, each of which are represented by particles of finite size. One application might include red blood cells adhering together to form rouleaux, which are chains of red blood cells that are found in different parts of the circulatory system. Other potential applications include adhesion of platelets to a blood vessel wall or mechanical heart valve, which is a precursor of thrombosis formation, or adhesion of cancer cells to organ walls in the lymphatic, circulatory, digestive or pulmonary systems.

  11. Pegylated polystyrene particles as a model system for artificial cells

    NARCIS (Netherlands)

    Meng, Fenghua; Engbers, Gerard H.M.; Gessner, Andrea; Müller, Reiner H.; Feijen, Jan

    2004-01-01

    Pegylated polystyrene particles (PS-PEG) were prepared as a model system for artificial cells, by modification of carboxyl polystyrene particles (PS-COOH) with homo- and hetero-bifunctional polyethylene glycols (PEG, MW 1500, 3400, and 5000) containing an amino end group for immobilization and an am

  12. Corrosion Studies of Platinum Nano-Particles for Fuel Cells

    DEFF Research Database (Denmark)

    Shim, Signe Sarah

    The main focus of the present thesis is on corrosion and prevention of corrosion of platinum particles supported on carbon. This is important for instance in connection with start up and shutdown of fuel cells. The degradation mechanism of platinum particles supported on carbon has been...

  13. Aortic calcified particles modulate valvular endothelial and interstitial cells.

    Science.gov (United States)

    van Engeland, Nicole C A; Bertazzo, Sergio; Sarathchandra, Padmini; McCormack, Ann; Bouten, Carlijn V C; Yacoub, Magdi H; Chester, Adrian H; Latif, Najma

    Normal and calcified human valve cusps, coronary arteries, and aortae harbor spherical calcium phosphate microparticles of identical composition and crystallinity, and their role remains unknown. The objective was to examine the direct effects of isolated calcified particles on human valvular cells. Calcified particles were isolated from healthy and diseased aortae, characterized, quantitated, and applied to valvular endothelial cells (VECs) and interstitial cells (VICs). Cell differentiation, viability, and proliferation were analyzed. Particles were heterogeneous, differing in size and shape, and were crystallized as calcium phosphate. Diseased donors had significantly more calcified particles compared to healthy donors (Pparticles from healthy and diseased donors. VECs treated with calcified particles showed a significant decrease in CD31 and VE-cadherin and an increase in von Willebrand factor expression, Pparticles. Isolated calcified particles from human aortae are not innocent bystanders but induce a phenotypical and pathological change of VECs and VICs characteristic of activated and pathological cells. Therapy tailored to reduce these calcified particles should be investigated. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Lineage mapper: A versatile cell and particle tracker

    Science.gov (United States)

    Chalfoun, Joe; Majurski, Michael; Dima, Alden; Halter, Michael; Bhadriraju, Kiran; Brady, Mary

    2016-11-01

    The ability to accurately track cells and particles from images is critical to many biomedical problems. To address this, we developed Lineage Mapper, an open-source tracker for time-lapse images of biological cells, colonies, and particles. Lineage Mapper tracks objects independently of the segmentation method, detects mitosis in confluence, separates cell clumps mistakenly segmented as a single cell, provides accuracy and scalability even on terabyte-sized datasets, and creates division and/or fusion lineages. Lineage Mapper has been tested and validated on multiple biological and simulated problems. The software is available in ImageJ and Matlab at isg.nist.gov.

  15. Quantitative analysis of particles, genomes and infectious particles in supernatants of haemorrhagic fever virus cell cultures

    Directory of Open Access Journals (Sweden)

    Hedlund Kjell-Olof

    2011-02-01

    Full Text Available Abstract Information on the replication of viral haemorrhagic fever viruses is not readily available and has never been analysed in a comparative approach. Here, we compared the cell culture growth characteristics of haemorrhagic fever viruses (HFV, of the Arenaviridae, Filoviridae, Bunyaviridae, and Flavivridae virus families by performing quantitative analysis of cell culture supernatants by (i electron microscopy for the quantification of virus particles, (ii quantitative real time PCR for the quantification of genomes, and (iii determination of focus forming units by coating fluorescent antibodies to infected cell monolayers for the quantification of virus infectivity. The comparative analysis revealed that filovirus and RVFV replication results in a surplus of genomes but varying degrees of packaging efficiency and infectious particles. More efficient replication and packaging was observed for Lassa virus, and Dengue virus resulting in a better yield of infectious particles while, YFV turned out to be most efficient with only 4 particles inducing one FFU. For Crimean-Congo haemorrhagic fever virus (CCHFV a surplus of empty shells was observed with only one in 24 particles equipped with a genome. The complete particles turned out to be extraordinarily infectious.

  16. Biological effects of atmospheric particles on human bronchial epithelial cells. Comparison with diesel exhaust particles.

    Science.gov (United States)

    Baulig, Augustin; Sourdeval, Matthieu; Meyer, Martine; Marano, Francelyne; Baeza-Squiban, Armelle

    2003-01-01

    Epidemiological studies have associated the increase of respiratory disorders with high levels of ambient particulate matter (PM) levels although the underlying biological mechanisms are unclear. PM are a complex mixture of particles with different origins but in urban areas, they mainly contain soots from transport like Diesel exhaust particles (DEP). In order to determine whether PM biological effects can be explained by the presence of DEP, the effects of urban PM, DEP and carbon black particles (CB) were compared on a human bronchial epithelial cell line (16-HBE14o-). Two types of PM were used : reference material (RPM) and PM with an aerodynamic diameter particles. However, DEP and to a lower extent PM inhibited cell proliferation, induced the release of a pro-inflammatory cytokine, GM-CSF, and generated a pro-oxidant state as shown by the increased intracellular peroxides production. By contrast, CB never induced such effects. Nevertheless CB are more endocytosed than DEP whereas PM are the less endocytosed particles. In conclusion, PM induced to a lower extent the same biological effects than DEP in 16-HBE cells suggesting that particle characteristics should be thoroughly considered in order to clearly correlate adverse effects of PM to their composition and to clarify the role of DEP in PM effects.

  17. An incompressible two-dimensional multiphase particle-in-cell model for dense particle flows

    Energy Technology Data Exchange (ETDEWEB)

    Snider, D.M. [SAIC, Albuquerque, NM (United States); O`Rourke, P.J. [Los Alamos National Lab., NM (United States); Andrews, M.J. [Texas A and M Univ., College Station, TX (United States). Dept. of Mechanical Engineering

    1997-06-01

    A two-dimensional, incompressible, multiphase particle-in-cell (MP-PIC) method is presented for dense particle flows. The numerical technique solves the governing equations of the fluid phase using a continuum model and those of the particle phase using a Lagrangian model. Difficulties associated with calculating interparticle interactions for dense particle flows with volume fractions above 5% have been eliminated by mapping particle properties to a Eulerian grid and then mapping back computed stress tensors to particle positions. This approach utilizes the best of Eulerian/Eulerian continuum models and Eulerian/Lagrangian discrete models. The solution scheme allows for distributions of types, sizes, and density of particles, with no numerical diffusion from the Lagrangian particle calculations. The computational method is implicit with respect to pressure, velocity, and volume fraction in the continuum solution thus avoiding courant limits on computational time advancement. MP-PIC simulations are compared with one-dimensional problems that have analytical solutions and with two-dimensional problems for which there are experimental data.

  18. A gas cell for stopping, storing and polarizing radioactive particles

    CERN Document Server

    Sytema, A; Böll, O; Chernowitz, D; Dijck, E A; Grasdijk, J O; Hoekstra, S; Jungmann, K; Mathavan, S C; Meinema, C; Mohanty, A; Müller, S E; Portela, M Nuñez; Onderwater, C J G; Pijpker, C; Willmann, L; Wilschut, H W

    2016-01-01

    A radioactive beam of 20Na is stopped in a gas cell filled with Ne gas. The stopped particles are polarized by optical pumping. The degree of polarization that can be achieved is studied. A maximum polarization of 50% was found. The dynamic processes in the cell are described with a phenomenological model.

  19. A gas cell for stopping, storing and polarizing radioactive particles

    NARCIS (Netherlands)

    Sytema, Auke; van den Berg, Joost; Böll, Oliver; Chernowitz, Daniel; Dijck, Elwin; Grasdijk, Jan; Hoekstra, Steven; Jungmann, Klaus-Peter; Chirayath Mathavan, Sreekanth; Meinema, Jacoba Roelien; Mueller, Stefan E.; Portela, M. N.; Onderwater, Cornelis; Pijpker, Coen; Willmann, Lorenz; Wilschut, H. W.

    2016-01-01

    A radioactive beam of Na-20 is stopped in a gas cell filled with Ne gas. The stopped particles are polarized by optical pumping. The degree of polarization that can be achieved is studied. A maximum polarization of 50% was found. The dynamic processes in the cell are described with a phenomenologica

  20. Intracellular particle tracking as a tool for tumor cell characterization

    NARCIS (Netherlands)

    Li, Yixuan; Duits, Michel H.G.; Schnekenburger, Jürgen

    2009-01-01

    We studied the dynamics of two types of intracellular probe particles, ballistically injected latex spheres and endogenous granules, in tumor cell lines of differerent metastatic potential: breast tumor cells (MCF-7 malignant, MCF-10A benign) and pancreas adenocarcinoma (PaTu8988T malignant, PaTu898

  1. Sparse grid techniques for particle-in-cell schemes

    CERN Document Server

    Ricketson, Lee F

    2016-01-01

    We propose the use of sparse grids to accelerate particle-in-cell (PIC) schemes. By using the so-called `combination technique' from the sparse grids literature, we are able to dramatically increase the size of the spatial cells in multi-dimensional PIC schemes while paying only a slight penalty in grid-based error. The resulting increase in cell size allows us to reduce the statistical noise in the simulation without increasing total particle number. We present initial proof-of-principle results from test cases in two and three dimensions that demonstrate the new scheme's efficiency, both in terms of computation time and memory usage.

  2. Dosimetric Analyses of Single Particle Microbeam in Cell Irradiation Experiment

    Institute of Scientific and Technical Information of China (English)

    XU YongJian; JIANG Jiang; CHEN Lianyun; ZHAN Furu; YU Zengliang

    2008-01-01

    Single particle microbeam (SPM) is uniquely capable of delivering precisely the predefined number of charged particles to determined individual cells or sub-cellular targets in situ. It has been recognized as a powerful technique for unveiling ionization irradiation mechanisms of organism. This article describes some investigations on the irradiation quality of SPM of major world laboratories by means of Monte Carlo method based on dosimetry and microdosimetry. Those parameters are helpful not only to improve SPM irradiating cell experiments but also to study the biological effects of cells irradiated by SPM.

  3. Sparse grid techniques for particle-in-cell schemes

    Science.gov (United States)

    Ricketson, L. F.; Cerfon, A. J.

    2017-02-01

    We propose the use of sparse grids to accelerate particle-in-cell (PIC) schemes. By using the so-called ‘combination technique’ from the sparse grids literature, we are able to dramatically increase the size of the spatial cells in multi-dimensional PIC schemes while paying only a slight penalty in grid-based error. The resulting increase in cell size allows us to reduce the statistical noise in the simulation without increasing total particle number. We present initial proof-of-principle results from test cases in two and three dimensions that demonstrate the new scheme’s efficiency, both in terms of computation time and memory usage.

  4. Targeting Prostate Cancer Stem Cells with Alpha-Particle Therapy

    Science.gov (United States)

    Ceder, Jens; Elgqvist, Jörgen

    2017-01-01

    Modern molecular and radiopharmaceutical development has brought the promise of tumor-selective delivery of antibody–drug conjugates to tumor cells for the diagnosis and treatment of primary and disseminated tumor disease. The classical mode of discourse regarding targeted therapy has been that the antigen targeted must be highly and homogenously expressed in the tumor cell population, and at the same time exhibit low expression in healthy tissue. However, there is increasing evidence that the reason cancer patients are not cured by current protocols is that there exist subpopulations of cancer cells that are resistant to conventional therapy including radioresistance and that these cells express other target antigens than the bulk of the tumor cells. These types of cells are often referred to as cancer stem cells (CSCs). The CSCs are tumorigenic and have the ability to give rise to all types of cells found in a cancerous disease through the processes of self-renewal and differentiation. If the CSCs are not eradicated, the cancer is likely to recur after therapy. Due to some of the characteristics of alpha particles, such as short path length and high density of energy depositions per distance traveled in tissue, they are especially well suited for use in targeted therapies against microscopic cancerous disease. The characteristics of alpha particles further make it possible to minimize the irradiation of non-targeted surrounding healthy tissue, but most importantly, make it possible to deliver high-absorbed doses locally and therefore eradicating small tumor cell clusters on the submillimeter level, or even single tumor cells. When alpha particles pass through a cell, they cause severe damage to the cell membrane, cytoplasm, and nucleus, including double-strand breaks of DNA that are very difficult to repair for the cell. This means that very few hits to a cell by alpha particles are needed in order to cause cell death, enabling killing of cells, such as CSCs

  5. Measuring Landau damping in Particle-in-Cell simulations using particles of different charge-weights

    Science.gov (United States)

    Ren, C.; Sarkar, A.; Cao, Y.-X.; Huang, M. C.; Li, J.

    2016-10-01

    We study whether putting more particles in ``region of interest (ROI)'' in phase space can efficiently increase Particle-in-Cell (PIC) simulation accuracy. We use Landau damping of a plasma wave as a figure of merit and set the ROI near the phase velocity of the wave. Improvement in Landau damping rate measurement is observed in 1D PIC simulations when employing more particles in the ROI but the effect is not monotonic. This is partly due to energy transfer from particles of large charge weights to those of smaller weights through the electric fields. Possible strategies to mitigate the energy transfer will also be discussed. This work is supported by the National Science Foundation under Grant No. PHY-1314734 and by the Department of Energy under Grant No. DE-SC0012316.

  6. Speeding Up Simulations By Slowing Down Particles: Speed-Limited Particle-In-Cell Simulation

    CERN Document Server

    Werner, Gregory R

    2015-01-01

    Particle-in-cell (PIC) simulation is often impractical for the same reason that it is powerful: it includes too much physics. Sometimes the mere ability to simulate physics on small length or time scales requires those scales to be resolved (by the cell size and timestep) to avoid instability, even when the effects at those scales contribute negligibly to the phenomenon motivating the simulation. For example, a timestep larger than the inverse plasma frequency will often result in unphysical growth of plasma oscillations, even in simulations where plasma oscillations should not arise at all. Larger timesteps are possible in simulations based on reduced physics models, such as MHD or gyrokinetics, or in simulations with implicit time-advances. A new method, speed-limited PIC (SLPIC) simulation, allows larger timesteps without reduced physics and with an explicit time-advance. The SLPIC method slows down fast particles while still accurately representing the particle distribution. SLPIC is valid when fields and...

  7. Cell-cell transmission of VSV-G pseudotyped lentivector particles.

    Directory of Open Access Journals (Sweden)

    Amy M Skinner

    Full Text Available Many replicating viruses, including HIV-1 and HTLV-1, are efficiently transmitted from the cell surface of actively infected cells upon contact with bystander cells. In a previous study, we reported the prolonged cell surface retention of VSV-G replication-deficient pseudotyped lentivector prior to endocytic entry. However, the competing kinetics of cell surface versus dissociation, neutralization or direct transfer to other cells have received comparatively little attention. Here we demonstrate that the relative efficiency of cell-cell surface transmission can outpace "cell-free" transduction at limiting vector input. This coincides with the prolonged half-life of cell bound vector but occurs, unlike HTLV-1, without evidence for particle aggregation. These studies suggest that cell-surface attachment stabilizes particles and alters neutralization kinetics. Our experiments provide novel insight into the underexplored cell-cell transmission of pseudotyped particles.

  8. Microfluidic-Based Synthesis of Hydrogel Particles for Cell Microencapsulation and Cell-Based Drug Delivery

    Directory of Open Access Journals (Sweden)

    Jiandi Wan

    2012-04-01

    Full Text Available Encapsulation of cells in hydrogel particles has been demonstrated as an effective approach to deliver therapeutic agents. The properties of hydrogel particles, such as the chemical composition, size, porosity, and number of cells per particle, affect cellular functions and consequently play important roles for the cell-based drug delivery. Microfluidics has shown unparalleled advantages for the synthesis of polymer particles and been utilized to produce hydrogel particles with a well-defined size, shape and morphology. Most importantly, during the encapsulation process, microfluidics can control the number of cells per particle and the overall encapsulation efficiency. Therefore, microfluidics is becoming the powerful approach for cell microencapsulation and construction of cell-based drug delivery systems. In this article, I summarize and discuss microfluidic approaches that have been developed recently for the synthesis of hydrogel particles and encapsulation of cells. I will start by classifying different types of hydrogel material, including natural biopolymers and synthetic polymers that are used for cell encapsulation, and then focus on the current status and challenges of microfluidic-based approaches. Finally, applications of cell-containing hydrogel particles for cell-based drug delivery, particularly for cancer therapy, are discussed.

  9. Multigrid Particle-in-cell Simulations of Plasma Microturbulence

    Energy Technology Data Exchange (ETDEWEB)

    J.L.V. Lewandowski

    2003-06-17

    A new scheme to accurately retain kinetic electron effects in particle-in-cell (PIC) simulations for the case of electrostatic drift waves is presented. The splitting scheme, which is based on exact separation between adiabatic and on adiabatic electron responses, is shown to yield more accurate linear growth rates than the standard df scheme. The linear and nonlinear elliptic problems that arise in the splitting scheme are solved using a multi-grid solver. The multi-grid particle-in-cell approach offers an attractive path, both from the physics and numerical points of view, to simulate kinetic electron dynamics in global toroidal plasmas.

  10. Magnetic tweezers for manipulation of magnetic particles in single cells

    Science.gov (United States)

    Ebrahimian, H.; Giesguth, M.; Dietz, K.-J.; Reiss, G.; Herth, S.

    2014-02-01

    Magnetic tweezers gain increasing interest for applications in biology. Here, a setup of magnetic tweezers is introduced using micropatterned conducting lines on transparent glass slides. Magnetic particles of 1 μm diameter were injected in barley cell vacuoles using a microinject system under microscopic control. Time dependent tracking of the particles after application of a magnetic field was used to determine the viscosity of vacuolar sap in vivo relative to water and isolated vacuolar fluid. The viscosity of vacuolar sap in cells was about 2-fold higher than that of extracted vacuolar fluid and 5 times higher than that of water.

  11. Alpha-particles induce autophagy in multiple myeloma cells

    Directory of Open Access Journals (Sweden)

    Joelle Marcelle Gaschet

    2015-10-01

    Full Text Available Objectives: Radiations emitted by the radionuclides in radioimmunotherapy (RIT approaches induce direct killing of the targeted cells as well as indirect killing through bystander effect. Our research group is dedicated to the development of α-RIT, i.e RIT using α-particles especially for the treatment of multiple myeloma (MM. γ-irradiation and β-irradiation have been shown to trigger apoptosis in tumor cells. Cell death mode induced by 213Bi α-irradiation appears more controversial. We therefore decided to investigate the effects of 213Bi on MM cell radiobiology, notably cell death mechanisms as well as tumor cell immunogenicity after irradiation.Methods: Murine 5T33 and human LP-1 multiple myeloma (MM cell lines were used to study the effects of such α-particles. We first examined the effects of 213Bi on proliferation rate, double strand DNA breaks, cell cycle and cell death. Then, we investigated autophagy after 213Bi irradiation. Finally, a co-culture of dendritic cells (DC with irradiated tumour cells or their culture media was performed to test whether it would induce DC activation.Results: We showed that 213Bi induces DNA double strand breaks, cell cycle arrest and autophagy in both cell lines but we detected only slight levels of early apoptosis within the 120 hours following irradiation in 5T33 and LP-1. Inhibition of autophagy prevented 213Bi induced inhibition of proliferation in LP-1 suggesting that this mechanism is involved in cell death after irradiation. We then assessed the immunogenicity of irradiated cells and found that irradiated LP-1 can activate DC through the secretion of soluble factor(s, however no increase in membrane or extracellular expression of danger associated molecular patterns (DAMPs was observed after irradiation.Conclusion: This study demonstrates that 213Bi induces mainly necrosis in MM cells, low levels of apoptosis and also autophagy that might be involved in tumor cell death.

  12. Particle-in-cell method in multiphase flow simulations

    Science.gov (United States)

    Zhang, Duan; Zou, Qisu; Vanderheyden, Brian

    2004-11-01

    In many disperse multiphase flows there is of great interest to know the deformations and the possibility of break up of the grains of the disperse phase. Some examples are the pneumatic transport of agriculture grains and the fragment-gas-structure interaction in an explosion. In these examples one needs to consider the stress states in both the disperse phase and the continuous phase. The use of Eulerian method encounters significant difficulties associated with numerical diffusion. The use of Lagrangian method encounters mesh-tangling problem. Expensive re-meshing procedures need to be done frequently. The particle-in-cell method possesses advantages of both methods while avoids their difficulties. A grain of the disperse phase is represented by particles. A particle in the method is not only a Lagrangian marker; it carries mass, momentum, energy and other quantities associated with the grain. Although the particle-in-cell method was invented in the sixties, its recent developments significantly enhanced its capabilities. In this presentation, we outline basic principles and numerical schemes of the particle-in-cell method and then provide examples of its applications. This work is supported by the U.S. Department of Energy. (LA-UR-04-4177)

  13. Review of cell and particle trapping in microfluidic systems

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, J.; Evander, M.; Hammarstroem, B. [Department of Measurement Technology and Industrial Electrical Engineering, Div. of Nanobiotechnology, Lund University, P.O. Box 118, Lund (Sweden); Laurell, T., E-mail: thomas.laurell@elmat.lth.se [Department of Measurement Technology and Industrial Electrical Engineering, Div. of Nanobiotechnology, Lund University, P.O. Box 118, Lund (Sweden)

    2009-09-07

    The ability to obtain ideal conditions for well-defined chemical microenvironments and controlled temporal chemical and/or thermal variations holds promise of high-resolution cell response studies, cell-cell interactions or e.g. proliferation conditions for stem cells. It is a major motivation for the rapid increase of lab-on-a-chip based cell biology research. In view of this, new chip-integrated technologies are at an increasing rate being presented to the research community as potential tools to offer spatial control and manipulation of cells in microfluidic systems. This is becoming a key area of interest in the emerging lab-on-a-chip based cell biology research field. This review focuses on the different technical approaches presented to enable trapping of particles and cells in microfluidic system.

  14. Ultrasound assisted particle and cell manipulation on-chip.

    Science.gov (United States)

    Mulvana, Helen; Cochran, Sandy; Hill, Martyn

    2013-11-01

    Ultrasonic fields are able to exert forces on cells and other micron-scale particles, including microbubbles. The technology is compatible with existing lab-on-chip techniques and is complementary to many alternative manipulation approaches due to its ability to handle many cells simultaneously over extended length scales. This paper provides an overview of the physical principles underlying ultrasonic manipulation, discusses the biological effects relevant to its use with cells, and describes emerging applications that are of interest in the field of drug development and delivery on-chip. © 2013.

  15. Ultrastructure of Zika virus particles in cell cultures

    Directory of Open Access Journals (Sweden)

    Debora Ferreira Barreto-Vieira

    2016-01-01

    Full Text Available Zika virus (ZIKV has infected thousands of Brazilian people and spread to other American countries since 2015. The introduction of ZIKV brought a strong impact to public health in Brazil. It is of utmost importance to identify a susceptible cell line that will enable the isolation and identification of the virus from patient samples, viral mass production, and testing of drug and vaccine candidates. Besides real-time reverse transcriptase polymerase chain reaction diagnosis for detecting the viral genome, virus isolation in cell lines was useful in order to study the structure of the viral particle and its behaviour inside cells. Analysis of ZIKV infected cell lines was achieved using transmission electron microscopy (TEM. Blood was obtained from a Brazilian patient during the first days after presenting with signs of the disease, and ZIKV from the patient’s blood was isolated in the C6/36 mosquito cell line. Afterwards, Vero cells were inoculated with the viral suspension, fixed six days after inoculation, embedded in polymers, and ultra-thin cut. Like dengue viruses, this flavivirus showed numerous virus particles present inside cellular vesicles thereby confirming the susceptibility of the Vero cell line to ZIKV replication. TEM is a unique technique available to make the virus visible.

  16. Ultrastructure of Zika virus particles in cell cultures.

    Science.gov (United States)

    Barreto-Vieira, Debora Ferreira; Barth, Ortrud Monika; Silva, Marcos Alexandre Nunes da; Santos, Carolina Cardoso; Santos, Aline da Silva; F, Joaquim Batista; Filippis, Ana Maria Bispo de

    2016-08-01

    Zika virus (ZIKV) has infected thousands of Brazilian people and spread to other American countries since 2015. The introduction of ZIKV brought a strong impact to public health in Brazil. It is of utmost importance to identify a susceptible cell line that will enable the isolation and identification of the virus from patient samples, viral mass production, and testing of drug and vaccine candidates. Besides real-time reverse transcriptase polymerase chain reaction diagnosis for detecting the viral genome, virus isolation in cell lines was useful in order to study the structure of the viral particle and its behaviour inside cells. Analysis of ZIKV infected cell lines was achieved using transmission electron microscopy (TEM). Blood was obtained from a Brazilian patient during the first days after presenting with signs of the disease, and ZIKV from the patient's blood was isolated in the C6/36 mosquito cell line. Afterwards, Vero cells were inoculated with the viral suspension, fixed six days after inoculation, embedded in polymers, and ultra-thin cut. Like dengue viruses, this flavivirus showed numerous virus particles present inside cellular vesicles thereby confirming the susceptibility of the Vero cell line to ZIKV replication. TEM is a unique technique available to make the virus visible.

  17. Ultrastructure of Zika virus particles in cell cultures

    Science.gov (United States)

    Barreto-Vieira, Debora Ferreira; Barth, Ortrud Monika; da Silva, Marcos Alexandre Nunes; Santos, Carolina Cardoso; Santos, Aline da Silva; F, Joaquim Batista; de Filippis, Ana Maria Bispo

    2016-01-01

    Zika virus (ZIKV) has infected thousands of Brazilian people and spread to other American countries since 2015. The introduction of ZIKV brought a strong impact to public health in Brazil. It is of utmost importance to identify a susceptible cell line that will enable the isolation and identification of the virus from patient samples, viral mass production, and testing of drug and vaccine candidates. Besides real-time reverse transcriptase polymerase chain reaction diagnosis for detecting the viral genome, virus isolation in cell lines was useful in order to study the structure of the viral particle and its behaviour inside cells. Analysis of ZIKV infected cell lines was achieved using transmission electron microscopy (TEM). Blood was obtained from a Brazilian patient during the first days after presenting with signs of the disease, and ZIKV from the patient’s blood was isolated in the C6/36 mosquito cell line. Afterwards, Vero cells were inoculated with the viral suspension, fixed six days after inoculation, embedded in polymers, and ultra-thin cut. Like dengue viruses, this flavivirus showed numerous virus particles present inside cellular vesicles thereby confirming the susceptibility of the Vero cell line to ZIKV replication. TEM is a unique technique available to make the virus visible. PMID:27581122

  18. The Energy Conserving Particle-in-Cell Method

    CERN Document Server

    Markidis, Stefano

    2011-01-01

    A new Particle-in-Cell (PIC) method, that conserves energy exactly, is presented. The particle equations of motion and the Maxwell's equations are differenced implicitly in time by the midpoint rule and solved concurrently by a Jacobian-free Newton Krylov (JFNK) solver. Several tests show that the finite grid instability is eliminated in energy conserving PIC simulations, and the method correctly describes the two-stream and Weibel instabilities, conserving exactly the total energy. The computational time of the energy conserving PIC method increases linearly with the number of particles, and it is rather insensitive to the number of grid points and time step. The kinetic enslavement technique can be effectively used to reduce the problem matrix size and the number of JFNK solver iterations.

  19. Accelerating particle-in-cell simulations using multilevel Monte Carlo

    Science.gov (United States)

    Ricketson, Lee

    2015-11-01

    Particle-in-cell (PIC) simulations have been an important tool in understanding plasmas since the dawn of the digital computer. Much more recently, the multilevel Monte Carlo (MLMC) method has accelerated particle-based simulations of a variety of systems described by stochastic differential equations (SDEs), from financial portfolios to porous media flow. The fundamental idea of MLMC is to perform correlated particle simulations using a hierarchy of different time steps, and to use these correlations for variance reduction on the fine-step result. This framework is directly applicable to the Langevin formulation of Coulomb collisions, as demonstrated in previous work, but in order to apply to PIC simulations of realistic scenarios, MLMC must be generalized to incorporate self-consistent evolution of the electromagnetic fields. We present such a generalization, with rigorous results concerning its accuracy and efficiency. We present examples of the method in the collisionless, electrostatic context, and discuss applications and extensions for the future.

  20. Classical Radiation Reaction in Particle-In-Cell Simulations

    CERN Document Server

    Vranic, Marija; Fonseca, Ricardo A; Silva, Luis O

    2015-01-01

    Under the presence of ultra high intensity lasers or other intense electromagnetic fields the motion of particles in the ultrarelativistic regime can be severely affected by radiation reaction. The standard particle-in-cell (PIC) algorithms do not include radiation reaction effects. Even though this is a well known mechanism, there is not yet a definite algorithm nor a standard technique to include radiation reaction in PIC codes. We have compared several models for the calculation of the radiation reaction force, with the goal of implementing an algorithm for classical radiation reaction in the Osiris framework, a state-of-the-art PIC code. The results of the different models are compared with standard analytical results, and the relevance/advantages of each model are discussed. Numerical issues relevant to PIC codes such as resolution requirements, application of radiation reaction to macro particles and computational cost are also addressed. The Landau and Lifshitz reduced model is chosen for implementatio...

  1. Flow properties of particles in a model annular shear cell

    Science.gov (United States)

    Wang, X.; Zhu, H. P.; Yu, A. B.

    2012-05-01

    In order to quantitatively investigate the mechanical and rheological properties of solid flow in a shear cell under conditions relevant to those in an annular cell, we performed a series of discrete particle simulations of slightly polydispersed spheres from quasi-static to intermediate flow regimes. It is shown that the average values of stress tensor components are uniformly distributed in the cell space away from the stationary walls; however, some degree of inhomogeneity in their spatial distributions does exist. A linear relationship between the (internal/external) shear and normal stresses prevails in the shear cell and the internal and external friction coefficients can compare well with each other. It is confirmed that annular shear cells are reasonably effective as a method of measuring particle flow properties. The so-called I-rheology proposed by Jop et al. [Nature (London) 441, 727 (2006)] is rigorously tested in this cell system. The results unambiguously display that the I-rheology can effectively describe the intermediate flow regime with a high correlation coefficient. However, significant deviations take place when it is applied to the quasi-static regime, which corresponds to very small values of inertial number.

  2. Load management strategy for Particle-In-Cell simulations in high energy particle acceleration

    Science.gov (United States)

    Beck, A.; Frederiksen, J. T.; Dérouillat, J.

    2016-09-01

    In the wake of the intense effort made for the experimental CILEX project, numerical simulation campaigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. In this paper, we compare the results given by different codes and point out algorithmic limitations both in terms of physical accuracy and computational performances. These limitations are illustrated in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-performance PIC code for high energy particle acceleration.

  3. Acoustic Devices for Particle and Cell Manipulation and Sensing

    Directory of Open Access Journals (Sweden)

    Yongqiang Qiu

    2014-08-01

    Full Text Available An emerging demand for the precise manipulation of cells and particles for applications in cell biology and analytical chemistry has driven rapid development of ultrasonic manipulation technology. Compared to the other manipulation technologies, such as magnetic tweezing, dielectrophoresis and optical tweezing, ultrasonic manipulation has shown potential in a variety of applications, with its advantages of versatile, inexpensive and easy integration into microfluidic systems, maintenance of cell viability, and generation of sufficient forces to handle particles, cells and their agglomerates. This article briefly reviews current practice and reports our development of various ultrasonic standing wave manipulation devices, including simple devices integrated with high frequency (>20 MHz ultrasonic transducers for the investigation of biological cells and complex ultrasonic transducer array systems to explore the feasibility of electronically controlled 2-D and 3-D manipulation. Piezoelectric and passive materials, fabrication techniques, characterization methods and possible applications are discussed. The behavior and performance of the devices have been investigated and predicted with computer simulations, and verified experimentally. Issues met during development are highlighted and discussed. To assist long term practical adoption, approaches to low-cost, wafer level batch-production and commercialization potential are also addressed.

  4. Slurm: An innovative Particle-in-Cell Method for Magnetohydrodynamics

    Science.gov (United States)

    Bacchini, Fabio; Olshevsky, Vyacheslav; Lapenta, Giovanni

    2016-10-01

    We present a new Particle-in-Cell method for plasma simulations. This is based on the original algorithm of FLIP-MHD, which uses a Lagrangian formulation of the macroscopic equations. A finite-difference approximation of the equations of motion is solved on a fixed (non-moving) grid, while convection of the quantities is modelled with the support of Lagrangian particles. Interpolation with first-order b-splines is used to project the conserved quantities from particles to the grid and back. In this work, we introduce two modifications of the original scheme. A particle volume evolution procedure is adopted to reduce the computational error, based on the Material Point Method for solid mechanics. The additional step introduces little to none computational diffusion and efficiently suppresses the so-called ringing instability, allowing the use of explicit time differencing. Furthermore, we eliminate the need for a Poisson solver in the magnetic field computation with the use of a vector potential. The vector potential evolution is modelled with a moving grid and interpolated to the fixed grid points to obtain a solenoidal magnetic field. The results of a number of HD and MHD tests show good agreement with the reference solutions and rather fast time and space convergence. Air Force Office of Scientific Research, Air Force Materiel Command, USAF under Award No. FA9550-14-1-0375. European Community's Seventh Framework Programme (FP7/2007-2013) via the DEEP-ER project under Grant Agreement No. 610476.

  5. 880 nanosecond particle in cell mover for the CDC 7600

    Energy Technology Data Exchange (ETDEWEB)

    Estabrook, K.; Tull, J. E.

    1977-10-04

    A very fast computational method of moving particles for one dimensional electrostatic plasma simulations using integer arithmetic is described. The cloud in cell method forms the basis of this technique. This paper is in the form of a compass compilable subroutine with comments and examples describing methods of using an entirely integer representation to gain up to an order of magnitude increase in speed over equivalent floating point Fortran coding. Integer arithmetic has several advantages over floating point arithmetic for one dimensional particle movers. The adds are much faster, and the binary numerical description allows the implementation of very simple boundary conditions if the simulation region extends from zero to a power of two. Furthermore, integer arithmetic makes very efficient use of each memory bit since there is no floating point exponent. Consequently, it becomes feasible and fast in long word length machines to pack the velocity and position of a particular particle into the same word, thus saving a factor of two in computer storage and/or 10. These advantages are combined with the fact that integer adds and logicals complete in only two computer cycles allowing nearly complete optimization of register and instruction interleaving. The measured timings on a CDC 7600 are 880 nanoseconds and 935 nanoseconds per particle for the periodic and general boundary condition sections respectively. Methods for adapting the technique to other computers are discussed.

  6. Particle-cell contact enhances antibacterial activity of silver nanoparticles.

    Directory of Open Access Journals (Sweden)

    Olesja Bondarenko

    Full Text Available BACKGROUND: It is generally accepted that antibacterial properties of Ag nanoparticles (AgNPs are dictated by their dissolved fraction. However, dissolution-based concept alone does not fully explain the toxic potency of nanoparticulate silver compared to silver ions. METHODOLOGY/PRINCIPAL FINDINGS: Herein, we demonstrated that the direct contact between bacterial cell and AgNPs' surface enhanced the toxicity of nanosilver. More specifically, cell-NP contact increased the cellular uptake of particle-associated Ag ions - the single and ultimate cause of toxicity. To prove that, we evaluated the toxicity of three different AgNPs (uncoated, PVP-coated and protein-coated to six bacterial strains: Gram-negative Escherichia coli, Pseudomonas fluorescens, P. putida and P. aeruginosa and Gram-positive Bacillus subtilis and Staphylococcus aureus. While the toxicity of AgNO3 to these bacteria varied only slightly (the 4-h EC50 ranged from 0.3 to 1.2 mg Ag/l, the 4-h EC50 values of protein-coated AgNPs for various bacterial strains differed remarkably, from 0.35 to 46 mg Ag/l. By systematically comparing the intracellular and extracellular free Ag(+ liberated from AgNPs, we demonstrated that not only extracellular dissolution in the bacterial test environment but also additional dissolution taking place at the particle-cell interface played an essential role in antibacterial action of AgNPs. The role of the NP-cell contact in dictating the antibacterial activity of Ag-NPs was additionally proven by the following observations: (i separation of bacterial cells from AgNPs by particle-impermeable membrane (cut-off 20 kDa, ∼4 nm significantly reduced the toxicity of AgNPs and (ii P. aeruginosa cells which tended to attach onto AgNPs, exhibited the highest sensitivity to all forms of nanoparticulate Ag. CONCLUSIONS/SIGNIFICANCE: Our findings provide new insights into the mode of antibacterial action of nanosilver and explain some discrepancies in this field

  7. Dissecting the cell entry pathway of dengue virus by single-particle tracking in living cells.

    Directory of Open Access Journals (Sweden)

    Hilde M van der Schaar

    2008-12-01

    Full Text Available Dengue virus (DENV is an enveloped RNA virus that causes the most common arthropod-borne infection worldwide. The mechanism by which DENV infects the host cell remains unclear. In this work, we used live-cell imaging and single-virus tracking to investigate the cell entry, endocytic trafficking, and fusion behavior of DENV. Simultaneous tracking of DENV particles and various endocytic markers revealed that DENV enters cells exclusively via clathrin-mediated endocytosis. The virus particles move along the cell surface in a diffusive manner before being captured by a pre-existing clathrin-coated pit. Upon clathrin-mediated entry, DENV particles are transported to Rab5-positive endosomes, which subsequently mature into late endosomes through acquisition of Rab7 and loss of Rab5. Fusion of the viral membrane with the endosomal membrane was primarily detected in late endosomal compartments.

  8. Optical separation and controllable delivery of cells from particle and cell mixture

    Directory of Open Access Journals (Sweden)

    Li Yuchao

    2015-11-01

    Full Text Available Cell separation and delivery have recently gained significant attention in biological and biochemical studies. In thiswork, an optical method for separation and controllable delivery of cells by using an abruptly tapered fiber probe is reported. By launching a laser beam at the wavelength of 980 nm into the fiber, a mixture of cells with sizes of ~5 and ~3 μm and poly(methyl methacrylate particles with size of 5 μm are separated into three chains along the direction of propagation of light. The cell and particle chains are delivered in three dimensions over 600 μm distance. Experimental results are interpreted by numerical simulations. Optical forces and forward migration velocities of different particles and cells are calculated and discussed.

  9. Model of cell response to {\\alpha}-particle radiation

    CERN Document Server

    Liu, Longjian

    2012-01-01

    Starting from a general equation for organism (or cell system) growth and attributing additional cell death rate (besides the natural rate) to therapy, we derive an equation for cell response to {\\alpha} radiation. Different from previous models that are based on statistical theory, the present model connects the consequence of radiation with the growth process of a biosystem and each variable or parameter has meaning regarding the cell evolving process. We apply this equation to model the dose response for {\\alpha}-particle radiation. It interprets the results of both high and low linear energy transfer (LET) radiations. When LET is high, the additional death rate is a constant, which implies that the localized cells are damaged immediately and the additional death rate is proportional to the number of cells present. While at low LET, the additional death rate includes a constant term and a linear term of radiation dose, implying that the damage to some cell nuclei has a time accumulating effect. This model ...

  10. Particle-in-Cell/Test-Particle Simulations of Technological Plasmas: Sputtering Transport in Capacitive Radio Frequency Discharges

    OpenAIRE

    Trieschmann, Jan; Schmidt, Frederik; Mussenbrock, Thomas

    2016-01-01

    The paper provides a tutorial to the conceptual layout of a self-consistently coupled Particle-In-Cell/Test-Particle model for the kinetic simulation of sputtering transport in capacitively coupled plasmas at low gas pressures. It explains when a kinetic approach is actually needed and which numerical concepts allow for the inherent nonequilibrium behavior of the charged and neutral particles. At the example of a generic sputtering discharge both the fundamentals of the applied Monte Carlo me...

  11. Particle acceleration in sub-cycle optical cells

    CERN Document Server

    Terranova, F

    2014-01-01

    A single laser pulse with spot size smaller than half its wavelength ($w_0 < \\lambda/2$) can provide a net energy gain to ultra-relativistic particles. In this paper, we discuss the properties of an optical cell consisting of $N$ sub-cycle pulses that propagate in the direction perpendicular to the electron motion. We show that the energy gain produced by the cell is proportional to $N$ and it is sizable even for $\\mathcal{O}(1\\mathrm{ TW})$ pulses. The optical cell acts as a defocusing lens with chromatic aberration and can be treated as a linear component in conventional accelerators if the transverse size of the beam is of the order of $\\lambda$.

  12. Fractal Aggregation of Copper Particles using Electroless Cell

    Directory of Open Access Journals (Sweden)

    S.Q.Chishty

    2013-12-01

    Full Text Available A phenomenon In which the particles performing Brownian motion when hit the aggregates become the part of it is known as Diffusion limited aggregation (DLA, which produces a fractal shape. Experimental efforts are discussed through which some DLA shapes arc obtained. For this purpose different electrolytic solutions are used. Electro less cells are also designed and constructed using standard methods. The cells have to be flexible in the sense that changing of plates and solutions should be easier for photography. We used compounds of copper,. for growth of fractals. Within a very short time metallic dendrites appeared in the cell at different operating conditions. These images were photographed, while desired branching structures in copper sulphate solution were seen. Results thus obtained are compared with the growth of DLA.

  13. Particle Trajectories in Rotating Wall Cell Culture Devices

    Science.gov (United States)

    Ramachandran N.; Downey, J. P.

    1999-01-01

    Cell cultures are extremely important to the medical community since such cultures provide an opportunity to perform research on human tissue without the concerns inherent in experiments on individual humans. Development of cells in cultures has been found to be greatly influenced by the conditions of the culture. Much work has focused on the effect of the motions of cells in the culture relative to the solution. Recently rotating wall vessels have been used with success in achieving improved cellular cultures. Speculation and limited research have focused on the low shear environment and the ability of rotating vessels to keep cells suspended in solution rather than floating or sedimenting as the primary reasons for the improved cellular cultures using these devices. It is widely believed that the cultures obtained using a rotating wall vessel simulates to some degree the effect of microgravity on cultures. It has also been speculated that the microgravity environment may provide the ideal acceleration environment for culturing of cellular tissues due to the nearly negligible levels of sedimentation and shear possible. This work predicts particle trajectories of cells in rotating wall vessels of cylindrical and annular design consistent with the estimated properties of typical cellular cultures. Estimates of the shear encountered by cells in solution and the interactions with walls are studied. Comparisons of potential experiments in ground and microgravity environments are performed.

  14. GEMPIC: Geometric ElectroMagnetic Particle-In-Cell Methods

    CERN Document Server

    Kraus, Michael; Morrison, Philip J; Sonnendrücker, Eric

    2016-01-01

    We present a novel framework for Finite Element Particle-in-Cell methods based on the discretization of the underlying Hamiltonian structure of the Vlasov-Maxwell system. We derive a semi-discrete Poisson bracket, which satisfies the Jacobi identity , and apply Hamiltonian splitting schemes for time integration. Techniques from Finite Element Exterior Calculus ensure conservation of the divergence of the magnetic field and Gauss' law as well as stability of the field solver. The resulting methods are gauge-invariant, feature exact charge conservation and show excellent long-time energy and momentum behavior.

  15. Particle-in-cell Simulations with Kinetic Electrons

    Energy Technology Data Exchange (ETDEWEB)

    J.L.V. Lewandowski

    2004-02-12

    A new scheme, based on an exact separation between adiabatic and nonadiabatic electron responses, for particle-in-cell (PIC) simulations of drift-type modes is presented. The (linear and nonlinear) elliptic equations for the scalar fields are solved using a multi-grid solver. The new scheme yields linear growth rates in excellent agreement with theory and it is shown to conserve energy well into the nonlinear regime. It is also demonstrated that simulations with few electrons are reliable and accurate, suggesting that large-scale, PIC simulations with electron dynamics in toroidal geometry (e.g., tokamaks and stellarators plasmas) are within reach of present-day massively parallel supercomputers.

  16. Induction of retrovirus particles in human testicular tumor (Tera-1) cell cultures: an electron microscopic study.

    Science.gov (United States)

    Bronson, D L; Fraley, E E; Fogh, J; Kalter, S S

    1979-08-01

    The Tera-1 and Tera-2 cell lines, established from germ-cell tumors of the human testis, were examined by electron microscopy for particles with the morphology of retroviruses. Extracellular and budding particles were observed at low frequencies only in cultures of Tera-1 cells that had been treated with 5-iodo-2'-deoxyuridine and dexamethasone. No particles were detected in untreated cultures of Tera-1 cells or in any preparations of Tera-2 cells.

  17. Classical radiation reaction in particle-in-cell simulations

    Science.gov (United States)

    Vranic, M.; Martins, J. L.; Fonseca, R. A.; Silva, L. O.

    2016-07-01

    Under the presence of ultra high intensity lasers or other intense electromagnetic fields the motion of particles in the ultrarelativistic regime can be severely affected by radiation reaction. The standard particle-in-cell (PIC) algorithms do not include radiation reaction effects. Even though this is a well known mechanism, there is not yet a definite algorithm nor a standard technique to include radiation reaction in PIC codes. We have compared several models for the calculation of the radiation reaction force, with the goal of implementing an algorithm for classical radiation reaction in the Osiris framework, a state-of-the-art PIC code. The results of the different models are compared with standard analytical results, and the relevance/advantages of each model are discussed. Numerical issues relevant to PIC codes such as resolution requirements, application of radiation reaction to macro particles and computational cost are also addressed. For parameters of interest where the classical description of the electron motion is applicable, all the models considered are shown to give comparable results. The Landau and Lifshitz reduced model is chosen for implementation as one of the candidates with the minimal overhead and no additional memory requirements.

  18. GPU Acceleration of Particle-In-Cell Methods

    Science.gov (United States)

    Cowan, Benjamin; Cary, John; Sides, Scott

    2016-10-01

    Graphics processing units (GPUs) have become key components in many supercomputing systems, as they can provide more computations relative to their cost and power consumption than conventional processors. However, to take full advantage of this capability, they require a strict programming model which involves single-instruction multiple-data execution as well as significant constraints on memory accesses. To bring the full power of GPUs to bear on plasma physics problems, we must adapt the computational methods to this new programming model. We have developed a GPU implementation of the particle-in-cell (PIC) method, one of the mainstays of plasma physics simulation. This framework is highly general and enables advanced PIC features such as high order particles and absorbing boundary conditions. The main elements of the PIC loop, including field interpolation and particle deposition, are designed to optimize memory access. We describe the performance of these algorithms and discuss some of the methods used. Work supported by DARPA Contract No. W31P4Q-16-C-0009.

  19. Speed-limited particle-in-cell (SLPIC) simulation

    Science.gov (United States)

    Werner, Gregory; Cary, John; Jenkins, Thomas

    2016-10-01

    Speed-limited particle-in-cell (SLPIC) simulation is a new method for particle-based plasma simulation that allows increased timesteps in cases where the timestep is determined (e.g., in standard PIC) not by the smallest timescale of interest, but rather by an even smaller physical timescale that affects numerical stability. For example, SLPIC need not resolve the plasma frequency if plasma oscillations do not play a significant role in the simulation; in contrast, standard PIC must usually resolve the plasma frequency to avoid instability. Unlike fluid approaches, SLPIC retains a fully-kinetic description of plasma particles and includes all the same physical phenomena as PIC; in fact, if SLPIC is run with a PIC-compatible timestep, it is identical to PIC. However, unlike PIC, SLPIC can run stably with larger timesteps. SLPIC has been shown to be effective for finding steady-state solutions for 1D collisionless sheath problems, greatly speeding up computation despite a large ion/electron mass ratio. SLPIC is a relatively small modification of standard PIC, with no complexities that might degrade parallel efficiency (compared to PIC), and is similarly compatible with PIC field solvers and boundary conditions.

  20. GPU acceleration of particle-in-cell methods

    Science.gov (United States)

    Cowan, Benjamin; Cary, John; Meiser, Dominic

    2015-11-01

    Graphics processing units (GPUs) have become key components in many supercomputing systems, as they can provide more computations relative to their cost and power consumption than conventional processors. However, to take full advantage of this capability, they require a strict programming model which involves single-instruction multiple-data execution as well as significant constraints on memory accesses. To bring the full power of GPUs to bear on plasma physics problems, we must adapt the computational methods to this new programming model. We have developed a GPU implementation of the particle-in-cell (PIC) method, one of the mainstays of plasma physics simulation. This framework is highly general and enables advanced PIC features such as high order particles and absorbing boundary conditions. The main elements of the PIC loop, including field interpolation and particle deposition, are designed to optimize memory access. We describe the performance of these algorithms and discuss some of the methods used. Work supported by DARPA contract W31P4Q-15-C-0061 (SBIR).

  1. Particle-in-cell simulations of particle energization from low Mach number fast mode shocks

    CERN Document Server

    Park, Jaehong; Blackman, Eric G; Ren, Chuang; Siller, Robert

    2012-01-01

    Astrophysical shocks are often studied in the high Mach number limit but weakly compressive fast shocks can occur in magnetic reconnection outflows and are considered to be a site of particle energization in solar flares. Here we study the microphysics of such perpendicular, low Mach number collisionless shocks using two-dimensional particle-in-cell (PIC) simulations with a reduced ion/electron mass ratio and employ a moving wall boundary method for initial generation of the shock. This moving wall method allows for more control of the shock speed, smaller simulation box sizes, and longer simulation times than the commonly used fixed wall, reflection method of shock formation. Our results, which are independent of the shock formation method, reveal the prevalence shock drift acceleration (SDA) of both electron and ions in a purely perpendicular shock with Alfv\\'en Mach number $M_A=6.8$ and ratio of thermal to magnetic pressure $\\beta=8$. We determine the respective minimum energies required for electrons and ...

  2. Particle-in-Cell Codes for plasma-based particle acceleration

    CERN Document Server

    Pukhov, Alexander

    2016-01-01

    Basic principles of particle-in-cell (PIC ) codes with the main application for plasma-based acceleration are discussed. The ab initio full electromagnetic relativistic PIC codes provide the most reliable description of plasmas. Their properties are considered in detail. Representing the most fundamental model, the full PIC codes are computationally expensive. The plasma-based acceler- ation is a multi-scale problem with very disparate scales. The smallest scale is the laser or plasma wavelength (from one to hundred microns) and the largest scale is the acceleration distance (from a few centimeters to meters or even kilometers). The Lorentz-boost technique allows to reduce the scale disparity at the costs of complicating the simulations and causing unphysical numerical instabilities in the code. Another possibility is to use the quasi-static approxi- mation where the disparate scales are separated analytically.

  3. Ragweed subpollen particles of respirable size activate human dendritic cells.

    Directory of Open Access Journals (Sweden)

    Kitti Pazmandi

    Full Text Available Ragweed (Ambrosia artemisiifolia pollen grains, which are generally considered too large to reach the lower respiratory tract, release subpollen particles (SPPs of respirable size upon hydration. These SPPs contain allergenic proteins and functional NAD(PH oxidases. In this study, we examined whether exposure to SPPs initiates the activation of human monocyte-derived dendritic cells (moDCs. We found that treatment with freshly isolated ragweed SPPs increased the intracellular levels of reactive oxygen species (ROS in moDCs. Phagocytosis of SPPs by moDCs, as demonstrated by confocal laser-scanning microscopy, led to an up-regulation of the cell surface expression of CD40, CD80, CD86, and HLA-DQ and an increase in the production of IL-6, TNF-α, IL-8, and IL-10. Furthermore, SPP-treated moDCs had an increased capacity to stimulate the proliferation of naïve T cells. Co-culture of SPP-treated moDCs with allogeneic CD3(+ pan-T cells resulted in increased secretion of IFN-γ and IL-17 by T cells of both allergic and non-allergic subjects, but induced the production of IL-4 exclusively from the T cells of allergic individuals. Addition of exogenous NADPH further increased, while heat-inactivation or pre-treatment with diphenyleneiodonium (DPI, an inhibitor of NADPH oxidases, strongly diminished, the ability of SPPs to induce phenotypic and functional changes in moDCs, indicating that these processes were mediated, at least partly, by the intrinsic NAD(PH oxidase activity of SPPs. Collectively, our data suggest that inhaled ragweed SPPs are fully capable of activating dendritic cells (DCs in the airways and SPPs' NAD(PH oxidase activity is involved in initiation of adaptive immune responses against innocuous pollen proteins.

  4. Guiding plant virus particles to integrin-displaying cells

    Science.gov (United States)

    Hovlid, Marisa L.; Steinmetz, Nicole F.; Laufer, Burkhardt; Lau, Jolene L.; Kuzelka, Jane; Wang, Qian; Hyypiä, Timo; Nemerow, Glen R.; Kessler, Horst; Manchester, Marianne; Finn, M. G.

    2012-05-01

    Viral nanoparticles (VNPs) are structurally regular, highly stable, tunable nanomaterials that can be conveniently produced in high yields. Unmodified VNPs from plants and bacteria generally do not show tissue specificity or high selectivity in binding to or entry into mammalian cells. They are, however, malleable by both genetic and chemical means, making them useful scaffolds for the display of large numbers of cell- and tissue-targeting ligands, imaging moieties, and/or therapeutic agents in a well-defined manner. Capitalizing on this attribute, we modified the genetic sequence of the Cowpea mosaic virus (CPMV) coat protein to display an RGD oligopeptide sequence derived from human adenovirus type 2 (HAdV-2). Concurrently, wild-type CPMV was modified via NHS acylation and Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC) chemistry to attach an integrin-binding cyclic RGD peptide. Both types of particles showed strong and selective affinity for several different cancer cell lines that express RGD-binding integrin receptors.Viral nanoparticles (VNPs) are structurally regular, highly stable, tunable nanomaterials that can be conveniently produced in high yields. Unmodified VNPs from plants and bacteria generally do not show tissue specificity or high selectivity in binding to or entry into mammalian cells. They are, however, malleable by both genetic and chemical means, making them useful scaffolds for the display of large numbers of cell- and tissue-targeting ligands, imaging moieties, and/or therapeutic agents in a well-defined manner. Capitalizing on this attribute, we modified the genetic sequence of the Cowpea mosaic virus (CPMV) coat protein to display an RGD oligopeptide sequence derived from human adenovirus type 2 (HAdV-2). Concurrently, wild-type CPMV was modified via NHS acylation and Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC) chemistry to attach an integrin-binding cyclic RGD peptide. Both types of particles showed strong and selective affinity

  5. Human Bronchial Epithelial Cell Response to Heavy Particle Exposure

    Science.gov (United States)

    Story, Michael; Ding, Liang-Hao; Minna, John; Park, Seong-mi; Peyton, Michael; Larsen, Jill

    2012-07-01

    A battery of non-oncogenically immortalized human bronchial epithelial cells (HBECs) are being used to examine the molecular changes that lead to lung carcinogenesis after exposure to heavy particles found in the free space environment. The goal is to ultimately identify biomarkers of radioresponse that can be used for prediction of carcinogenic risk for fatal lung cancer. Our initial studies have focused on the cell line HBEC3 KT and the isogenic variant HBEC3 KTR53, which overexpresses the RASv12 mutant and where p53 has been knocked down by shRNA, and is considered to be a more oncogenically progressed variant. We have previously described the response of HBEC3 KT at the cellular and molecular level, however, the focus here is on the rate of cellular transformation after HZE radiation exposure and the molecular changes in transformed cells. When comparing the two cell lines we find that there is a maximum rate of cellular transformation at 0.25 Gy when cells are exposed to 1 GeV Fe particles, and, for the HBEC3 KTR53 there are multiple pathways upregulated that promote anchorage independent growth including the mTOR pathway, the TGF-1 pathway, RhoA signaling and the ERK/MAPK pathway as early as 2 weeks after radiation. This does not occur in the HBEC3 KT cell line. Transformed HBEC3 KT cells do not show any morphologic or phenotypic changes when grown as cell cultures. HBEC3 KTR53 cells on the other hand show substantial changes in morphology from a cobblestone epithelial appearance to a mesenchymal appearance with a lack of contact inhibition. This epithelial to mesenchymal change in morphology is accompanied by the expression of vimentin and a reduction in the expression of E-cadherin, which are hallmarks of epithelial to mesenchymal transition. Interestingly, for HBEC3 KT transformed cells there are no mutations in the p53 gene, 2 of 15 clones were found to be heterozygous for the RASV12 mutation, and 3 of 15 clones expressed high levels of BigH3, a TGFB

  6. Measuring the mass, density, and size of particles and cells using a suspended microchannel resonator

    Science.gov (United States)

    Godin, Michel; Bryan, Andrea K.; Burg, Thomas P.; Babcock, Ken; Manalis, Scott R.

    2007-09-01

    We demonstrate the measurement of mass, density, and size of cells and nanoparticles using suspended microchannel resonators. The masses of individual particles are quantified as transient frequency shifts, while the particles transit a microfluidic channel embedded in the resonating cantilever. Mass histograms resulting from these data reveal the distribution of a population of heterogeneously sized particles. Particle density is inferred from measurements made in different carrier fluids since the frequency shift for a particle is proportional to the mass difference relative to the displaced solution. We have characterized the density of polystyrene particles, Escherichia coli, and human red blood cells with a resolution down to 10-4g/cm3.

  7. A DLM/FD/IB Method for Simulating Cell/Cell and Cell/Particle Interaction in Microchannels

    Institute of Scientific and Technical Information of China (English)

    Tsorng-Whay PAN; Lingling SHI; Roland GLOWINSKI

    2010-01-01

    A spring model is used to simulate the skeleton structure of the red blood cell(RBC)membrane and to study the red blood cell(RBC)rheology in Poiseuille flow with an immersed boundary method.The lateral migration properties of many cells in Poiseuille flow have been investigated.The authors also combine the above methodology with a distributed Lagrange multiplier/fictitious domain method to simulate the interaction of cells and neutrally buoyant particles in a microchannel for studying the margination of particles.

  8. Exactly energy conserving semi-implicit particle in cell formulation

    Science.gov (United States)

    Lapenta, Giovanni

    2017-04-01

    We report a new particle in cell (PIC) method based on the semi-implicit approach. The novelty of the new method is that unlike any of its semi-implicit predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. Recent research has presented fully implicit methods where energy conservation is obtained as part of a non-linear iteration procedure. The new method (referred to as Energy Conserving Semi-Implicit Method, ECSIM), instead, does not require any non-linear iteration and its computational cycle is similar to that of explicit PIC. The properties of the new method are: i) it conserves energy exactly to round-off for any time step or grid spacing; ii) it is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency and allowing the user to select any desired time step; iii) it eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length; iv) the particle mover has a computational complexity identical to that of the explicit PIC, only the field solver has an increased computational cost. The new ECSIM is tested in a number of benchmarks where accuracy and computational performance are tested.

  9. Turbulence dissipation challenge: particle-in-cell simulations

    Science.gov (United States)

    Roytershteyn, V.; Karimabadi, H.; Omelchenko, Y.; Germaschewski, K.

    2015-12-01

    We discuss application of three particle in cell (PIC) codes to the problems relevant to turbulence dissipation challenge. VPIC is a fully kinetic code extensively used to study a variety of diverse problems ranging from laboratory plasmas to astrophysics. PSC is a flexible fully kinetic code offering a variety of algorithms that can be advantageous to turbulence simulations, including high order particle shapes, dynamic load balancing, and ability to efficiently run on Graphics Processing Units (GPUs). Finally, HYPERS is a novel hybrid (kinetic ions+fluid electrons) code, which utilizes asynchronous time advance and a number of other advanced algorithms. We present examples drawn both from large-scale turbulence simulations and from the test problems outlined by the turbulence dissipation challenge. Special attention is paid to such issues as the small-scale intermittency of inertial range turbulence, mode content of the sub-proton range of scales, the formation of electron-scale current sheets and the role of magnetic reconnection, as well as numerical challenges of applying PIC codes to simulations of astrophysical turbulence.

  10. Second order Gyrokinetic theory for Particle-In-Cell codes

    CERN Document Server

    Tronko, Natalia; Sonnendruecker, Eric

    2016-01-01

    The main idea of Gyrokinetic dynamical reduction consists in systematical removing of fastest scale of motion (the gyro motion) from plasma's dynamics, resulting in a considerable model simplification and gain of computing time. Gyrokinetic Maxwell-Vlasov system is broadly implemented in nowadays numerical experiments for modeling strongly magnetized plasma (both laboratory and astrophysical). Different versions of reduced set of equations exist depending on the construction of the Gyrokinetic reduction procedure and approximations assumed while their derivation. The purpose of this paper is to explicitly show the connection between the general second order gyrokinetic Maxwell-Vlasov system issued from the Modern Gyrokinetic theory derivation and the model currently implemented in global electromagnetic Particle in Cell code ORB5. Strictly necessary information about the Modern Gyrokinetic formalism is given together with the consistent derivation of the gyrokinetic Maxwell-Vlasov equations from the first pri...

  11. Particle-In-Cell Simulation of RFQ in SSC - Linac

    CERN Document Server

    Chen, Xiao; You-Jin, Yuan; Yong, Liu; Jia-Wen, Xia; Yuan-Rong, Lu; Batygin, Yuri

    2010-01-01

    A 52MHz Radio Frequency Quadrupole (RFQ) linear accelerator (linac) is designed to serve as an initial structure for the SSC-linac system (injector into Separated Sector Cyclotron). The designed injection and output energy are 3.5 keV/u and 143 keV/u, respectively. Beam dynamics study in RFQ was done using 3-dimensional particle-in-cell code BEAMPATH [1]. Simulation results show that this RFQ structure is characterized by stable value of beam transmission efficiency (at least 95%) for both zero-current mode and for space charge dominated regime. The beam accelerated in RFQ has good quality in both transversal and longitudinal directions, and could be easily accepted by Drift Tube Linac (DTL). Effects of vane errors and of the space charge on beam parameters are studied as well to define the engineering tolerance for RFQ vane machining and alignment.

  12. The degradation of potato virus M (PVM particles in plant cells

    Directory of Open Access Journals (Sweden)

    Anna Rudzińska-Langwald

    2014-02-01

    Full Text Available Degradation of potato virus M particles was observed in the cells of Solanum tuberosum, Solanum rostratum, Lycopersicon esculentum and Lycopersicon chilense plants infected with this virus. PVM particles found in the cytoplasm of infected parenchyma cells grouped together in the form of inclusions, often found near the tonoplast. The ends of the virus particles and the tonoplast came into close contact. Cytoplasmic protrusions containing PVM particles, reaching into vacuoles were formed in those places. In addition to a large central vacuole, small vacuoles were observed in cells containing PVM particles. Various stages of degradation of cytoplasmic protrusions were observed both in the large and small vacuoles.

  13. Advanced cell therapies: targeting, tracking and actuation of cells with magnetic particles.

    Science.gov (United States)

    Connell, John J; Patrick, P Stephen; Yu, Yichao; Lythgoe, Mark F; Kalber, Tammy L

    2015-01-01

    Regenerative medicine would greatly benefit from a new platform technology that enabled measurable, controllable and targeting of stem cells to a site of disease or injury in the body. Superparamagnetic iron-oxide nanoparticles offer attractive possibilities in biomedicine and can be incorporated into cells, affording a safe and reliable means of tagging. This review describes three current and emerging methods to enhance regenerative medicine using magnetic particles to guide therapeutic cells to a target organ; track the cells using MRI and assess their spatial localization with high precision and influence the behavior of the cell using magnetic actuation. This approach is complementary to the systemic injection of cell therapies, thus expanding the horizon of stem cell therapeutics.

  14. Addressing of LnCaP Cell Using Magnetic Particles Assisted Impedimetric Microelectrode.

    Science.gov (United States)

    Nguyen, Dung Thi Xuan; Tran, Trong Binh; Nguyen, Phuong-Diem; Min, Junhong

    2016-03-01

    In this study, we provide a facile, effective technique for a simple isolation and enrichment of low metastatic prostate tumor cell LNCaP using biocompatible, magnetic particles asissted impedimetric sensing system. Hydrophobic cell membrane anchors (BAM) were generated onto magnetic particles which diameters vary from 50 nm to 5 μm and were used to capture LNCaP cells from the suspension. Finally, magnetic particle-LNCaP complex were addressed onto the surface of the interdigitated microelectrode (IDM). Cell viability was monitored by our laboratory developed-technique Electrical Cell Substrate Impedance Sensing (ECIS). The results reavealed that 50 nm-magnetic particles showed best performance in terms of cell separation and cell viability. This technique provides a simple and efficient method for the direct addressing of LNCaP cell on the surface and enhances better understanding of cell behavior for cancer management in the near future.

  15. Correlation of Particle Traversals with Clonogenic Survival Using Cell-Fluorescent Ion Track Hybrid Detector

    Science.gov (United States)

    Dokic, Ivana; Niklas, Martin; Zimmermann, Ferdinand; Mairani, Andrea; Seidel, Philipp; Krunic, Damir; Jäkel, Oliver; Debus, Jürgen; Greilich, Steffen; Abdollahi, Amir

    2015-01-01

    Development of novel approaches linking the physical characteristics of particles with biological responses are of high relevance for the field of particle therapy. In radiobiology, the clonogenic survival of cells is considered the gold standard assay for the assessment of cellular sensitivity to ionizing radiation. Toward further development of next generation biodosimeters in particle therapy, cell-fluorescent ion track hybrid detector (Cell-FIT-HD) was recently engineered by our group and successfully employed to study physical particle track information in correlation with irradiation-induced DNA damage in cell nuclei. In this work, we investigated the feasibility of Cell-FIT-HD as a tool to study the effects of clinical beams on cellular clonogenic survival. Tumor cells were grown on the fluorescent nuclear track detector as cell culture, mimicking the standard procedures for clonogenic assay. Cell-FIT-HD was used to detect the spatial distribution of particle tracks within colony-initiating cells. The physical data were associated with radiation-induced foci as surrogates for DNA double-strand breaks, the hallmark of radiation-induced cell lethality. Long-term cell fate was monitored to determine the ability of cells to form colonies. We report the first successful detection of particle traversal within colony-initiating cells at subcellular resolution using Cell-FIT-HD. PMID:26697410

  16. Correlation of Particle Traversals with Clonogenic Survival Using Cell-Fluorescent Ion Track Hybrid Detector

    Directory of Open Access Journals (Sweden)

    Ivana eDokic

    2015-12-01

    Full Text Available Development of novel approaches linking the physical characteristics of particles with biological responses are of high relevance for the field of particle therapy. In radiobiology, the clonogenic survival of cells is considered the gold standard assay for assessment of cellular sensitivity to ionizing radiation. Towards further development of next generation biodosimeters in particle therapy, cell-fluorescent ion track hybrid detector (Cell-FIT-HD was recently engineered by our group and successfully employed to study physical particle track information in correlation with irradiation- induced DNA damage in cell nuclei. In this work, we investigated the feasibility of Cell-FIT-HD as a tool to study the effects of clinical beams on cellular clonogenic survival. Tumor cells were grown on the FNTD as cell culture, mimicking the standard procedures for clonogenic assay. Cell-FIT-HD was used to detect the spatial distribution of particle tracks within colony-initiating cells. The physical data were associated to radiation induced foci as surrogates for DNA double strand breakages (DSB, the hallmark of radiation ‐induced cell lethality. Long‐term cell fate was monitored to determine the ability of cells to form colonies. We report the first successful detection of particle traversal within colony-initiating cells at subcellular resolution using Cell-FIT-HD.

  17. Particle-in-Cell/Test-Particle Simulations of Technological Plasmas: Sputtering Transport in Capacitive Radio Frequency Discharges

    CERN Document Server

    Trieschmann, Jan; Mussenbrock, Thomas

    2016-01-01

    The paper provides a tutorial to the conceptual layout of a self-consistently coupled Particle-In-Cell/Test-Particle model for the kinetic simulation of sputtering transport in capacitively coupled plasmas at low gas pressures. It explains when a kinetic approach is actually needed and which numerical concepts allow for the inherent nonequilibrium behavior of the charged and neutral particles. At the example of a generic sputtering discharge both the fundamentals of the applied Monte Carlo methods as well as the conceptual details in the context of the sputtering scenario are elaborated on. Finally, two in the context of sputtering transport simulations often exploited assumptions, namely on the energy distribution of impinging ions as well as on the test particle approach, are validated for the proposed example discharge.

  18. Second order gyrokinetic theory for particle-in-cell codes

    Science.gov (United States)

    Tronko, Natalia; Bottino, Alberto; Sonnendrücker, Eric

    2016-08-01

    The main idea of the gyrokinetic dynamical reduction consists in a systematical removal of the fast scale motion (the gyromotion) from the dynamics of the plasma, resulting in a considerable simplification and a significant gain of computational time. The gyrokinetic Maxwell-Vlasov equations are nowadays implemented in for modeling (both laboratory and astrophysical) strongly magnetized plasmas. Different versions of the reduced set of equations exist, depending on the construction of the gyrokinetic reduction procedure and the approximations performed in the derivation. The purpose of this article is to explicitly show the connection between the general second order gyrokinetic Maxwell-Vlasov system issued from the modern gyrokinetic theory and the model currently implemented in the global electromagnetic Particle-in-Cell code ORB5. Necessary information about the modern gyrokinetic formalism is given together with the consistent derivation of the gyrokinetic Maxwell-Vlasov equations from first principles. The variational formulation of the dynamics is used to obtain the corresponding energy conservation law, which in turn is used for the verification of energy conservation diagnostics currently implemented in ORB5. This work fits within the context of the code verification project VeriGyro currently run at IPP Max-Planck Institut in collaboration with others European institutions.

  19. Exactly Energy Conserving Implicit Moment Particle in Cell Formulation

    CERN Document Server

    Lapenta, Giovanni

    2016-01-01

    We report a new particle in cell (PIC) method based on the implicit moment method (IMM). The novelty of the new method is that unlike any of its predecessors at the same time retains the explicit computational cycle and conserves energy exactly. Recent research has presented fully implicit methods where energy conservation is obtained as part of a non linear iteration procedure. The new method, referred to as Energy Conserving Implicit Moment Method (ECIMM), does not require any non linear iteration and its computational cycle is similar to that of explicit PIC. The properties of then new method are: i) it conserves energy exactly to round-off for any time step or grid spacing; ii) it is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency and allowing the user to select any desired time step; iii) it eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length. T...

  20. Hydrodynamics of interaction of particles (including cells) with surfaces

    Science.gov (United States)

    Duszyk, Marek; Doroszewski, Jan

    The study of the phenomena related to the motion of particles flowing in the proximity of the wall is pursued for purely cognitive reason as well as for some important practical purposes in various fields of technology, biology and medicine. When small spherical rigid particles move in the direction parallel to the surface their velocity is smaller than that of the fluid and depends on the ratio of the distance from the wall to the particle radius. The velocity of a particle falling down in a vertical cylinder is maximal in an eccentric position. A sphere in contact with the wall remains stationary. Translational velocity of spherical rigid particles the dimension of which are comparable to that of the tube is only slightly dependent of their lateral position. The differences in the flow parameters of deformable particles in comparison with rigid ones depend on the particle and fluid viscosity coefficient. When the particles move perpendicularly toward the wall, their velocity decreases as the particle approaches the surface. The change of particle velocity is inversely proportional to the gap. There are several theories explaining the influence of the channel diameter on the suspension viscosity (sigma phenomenon); a modern approach is based on the analysis of rheological properties of suspensions. The explanations of the Fahraeus effect (i.e. the fact that the concentration of particles flowing in a tube linking two containers are smaller than that in the containers) are based on non-uniform particle distribution in a transverse cross section and on the differences of velocities of particles and medium. The deviation of the velocity profile of a suspension of rigid particles flowing through a tube from the parabolic shape (blunting) does not depend on the flow velocity; as concerns deformable particles, however, this effect is the smaller the greater is the flow velocity. When the Reynolds number for particles is greater than 10 -3, there appears a component of

  1. Effects of Cell Type and Culture Media on Interleukin-6 Secretion in Response to Environmental Particles

    OpenAIRE

    Veranth, John M; Cutler, N. Shane; Kaser, Erin G.; Reilly, Christopher A.; Yost, Garold S.

    2007-01-01

    Cultured lung cells provide an alternative to animal exposures for comparing the effects of different types of air pollution particles. Studies of particulate matter in vitro have reported proinflammatory cytokine signaling in response to many types of environmental particles, but there have been few studies comparing identical treatments in multiple cell types or identical cells with alternative cell culture protocols. We compared soil-derived, diesel, coal fly ash, titanium dioxide, and kao...

  2. Needle-shaped polymeric particles induce transient disruption of cell membranes.

    Science.gov (United States)

    Doshi, Nishit; Mitragotri, Samir

    2010-08-06

    Nano- and microparticles of various shapes have recently been introduced for various drug-delivery applications. Shape of particles has been shown to have an impact on various processes including circulation, vascular adhesion and phagocytosis. Here, we assess the role of particle geometry and surface chemistry in their interactions with cell membranes. Using representative particles of different shape (spheres, elongated and flat particles), size (500 nm-1 microm) and surface chemistry (positively and negatively charged), we evaluated the response of endothelial cells to particles. While spherical and elliptical disc-shaped particles did not have an impact on cell spreading and motility, needle-shaped particles induced significant changes in the same. Further studies revealed that needle-shaped particles induced disruption of cell membranes as indicated by the release of lactate dehydrogenase and uptake of extracellular calcein. The effect of needle-shaped particles on cells was transient and was reversed over a time period of 1-48 h depending on particle parameters.

  3. Wood smoke particle sequesters cell iron to impact a biological effect.

    Science.gov (United States)

    The biological effect of an inorganic particle (i.e., silica) can be associated with a disruption in cell iron homeostasis. Organic compounds included in particles originating from combustion processes can also complex sources of host cell iron to disrupt metal homeostasis. We te...

  4. Necrosis of HepG2 cancer cells induced by the vibration of magnetic particles

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Biran [Laboratoire de Physique de la Matière Condensée (LPMC), CNRS UMR 7336, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice (France); Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, 28 Avenue de Valrose, F-06100 Nice (France); Bienvenu, Céline [Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, 28 Avenue de Valrose, F-06100 Nice (France); Mendez-Garza, Juan; Lançon, Pascal; Madeira, Alexandra [Laboratoire de Physique de la Matière Condensée (LPMC), CNRS UMR 7336, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice (France); Vierling, Pierre [Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, 28 Avenue de Valrose, F-06100 Nice (France); Di Giorgio, Christophe, E-mail: christophe.di-giorgio@unice.fr [Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, 28 Avenue de Valrose, F-06100 Nice (France); Bossis, Georges, E-mail: bossis@unice.fr [Laboratoire de Physique de la Matière Condensée (LPMC), CNRS UMR 7336, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice (France)

    2013-10-15

    Experiments of magnetolysis, i.e., destruction of cells induced with magnetic particles (MPs) submitted to the application of a magnetic field, were conducted on HepG2 cancer cells. We herein demonstrate the usefulness of combining anisotropic MPs with an alternative magnetic field in magnetolysis. Thus, the application of an alternative magnetic field of low frequency (a few Hertz) in the presence of anisotropic, submicronic particles allowed the destruction of cancer cells “in vitro”. We also show that a constant magnetic field is far less efficient than an oscillating one. Moreover, we demonstrate that, at equal particle volume, it is much more efficient to utilize spindle shaped particles rather than spherical ones. In order to get deeper insight into the mechanism of magnetolysis experiments, we performed a study by AFM, which strongly supports that the magnetic field induces the formation of clusters of particles becoming then large enough todamage cell membranes. - Highlights: • Magnetic force was applied on cancer cells through magnetic particles. • The penetration depth was predicted, both for spherical and ellipsoidal particles. • Alternative force was shown to damage the cells contrary to static force. • The effect of indentation of magnetic particles was compared to the one of AFM tips. • The damage was attributed to the formation of clusters of particles.

  5. Cytocompatibility of HeLa Cells to Nano-Sized Ceramics Particles.

    Science.gov (United States)

    Seitoku, Eri; Abe, Shigeaki; Kusaka, Teruo; Nakamura, Mariko; Inoue, Satoshi; Yoshida, Yasuhiro; Sano, Hidehiko

    2016-04-01

    In this study, we investigated the behaviors and cytocompatibility response of human cervical carcinoma (HeLa) cells expose to nano-sized particles. Cultivated cells exposed to titanium oxide and indium oxide nanoparticles remained highly viable. In the presence of copper oxide (CuO); however, the cells became seriously inflamed. To understand the mechanism by which CuO causes cell death, we evaluated cell death and apoptosis cytometry. CuO induced cells apoptosis more strongly than exposure to titania nanoparticles. Confocal fluorescence microscopy revealed that the nano-sized particles penetrate the cells.

  6. Magnetic particle motions within living cells. Measurement of cytoplasmic viscosity and motile activity.

    Science.gov (United States)

    Valberg, P A; Feldman, H A

    1987-01-01

    Submicrometer magnetic particles, ingested by cells and monitored via the magnetic fields they generate, provide an alternative to optical microscopy for probing movement and viscosity of living cytoplasm, and can be used for cells both in vitro and in vivo. We present methods for preparing lung macrophages tagged with magnetic particles for magnetometric study. Interpretation of the data involves fitting experimental remanent-field decay curves to nonlinear mechanistic models of intracellular particle motion. The model parameters are sensitive to mobility and apparent cytoplasmic viscosity experienced by particle-containing organelles. We present results of parameter estimation for intracellular particle behavior both within control cells and after (a) variable magnetization duration, (b) incubation with cytochalasin D, and (c) particle twisting by external fields. Magnetometric analysis showed cytoplasmic elasticity, dose-dependent motion inhibition by cytochalasin D, and a shear-thinning apparent viscosity. Images FIGURE 1 FIGURE 2 PMID:3676436

  7. Diesel exhaust particle-induced cell death of cultured normal human bronchial epithelial cells.

    Science.gov (United States)

    Matsuo, Mitsuyoshi; Shimada, Toshio; Uenishi, Rie; Sasaki, Naoko; Sagai, Masaru

    2003-04-01

    We investigated the effect of diesel exhaust particles (DEPs) on normal human bronchial epithelial (NHBE) cells. Inclusion of DEPs in culture media was lethal to NHBE cells. NHBE cells are more susceptible to DEPs than other normal human lung cells, normal human pulmonary artery endothelial cells and normal human embryonic lung fibroblasts. DEP-induced cell death was mainly due to necrosis. Using the fluorescence probes diacetoxymethyl 6-carboxy-3',6'-diacetoxy-2',7'-dichloro-3',6'-dideoxydihydrofluorescinate and 4,5-diaminofluorescein diacetate, it was observed that hydrogen peroxide and nitrogen monoxide, respectively, were generated within DEP-exposed NHBE cells. DEP cytotoxicity increased or decreased with an increase or decrease in the cellular level of reduced glutathione (GSH) by treatment with L-buthionine-(R,S)-sulfoximine or ethyl reduced glutathionate, respectively. In addition, DEPs themselves decreased the cellular level of GSH in a dose-dependent manner. Upon exposure of NHBE cells to high concentrations of DEPs, their cellular GSH was depleted almost throughout. Further, the following agents decreased DEP cytotoxicity: 1) antioxidants 2,2,5,7,8-pentamethylchroman-6-ol, ebselen, and N,N'-bis(salicylidene)ethylenediaminomanganese(II) dihydrate (EUK-8); 2) iron ion-chelating agents disodium bathophenanthrolinedisulfonate and desferrioxamine mesylate; 3) nitrogen monoxide synthase inhibitors N(G)-nitro-L-arginine methyl ester hydrochloride and N(G)-methyl-L-arginine acetate salt; and 4) an endocytosis inhibitor quinacrine. On the basis of these observations, the mechanism of DEP cytotoxicity toward NHBE cells is discussed.

  8. Natural mineral particles are cytotoxic to rainbow trout gill epithelial cells in vitro.

    Science.gov (United States)

    Michel, Christian; Herzog, Simon; de Capitani, Christian; Burkhardt-Holm, Patricia; Pietsch, Constanze

    2014-01-01

    Worldwide increases in fluvial fine sediment are a threat to aquatic animal health. Fluvial fine sediment is always a mixture of particles whose mineralogical composition differs depending on the sediment source and catchment area geology. Nonetheless, whether particle impact in aquatic organisms differs between mineral species remains to be investigated. This study applied an in vitro approach to evaluate cytotoxicity and uptake of four common fluvial mineral particles (quartz, feldspar, mica, and kaolin; concentrations: 10, 50, 250 mg L(-1)) in the rainbow trout epithelial gill cell line RTgill-W1. Cells were exposed for 24, 48, 72, and 96 h. Cytotoxicity assays for cell membrane integrity (propidium iodide assay), oxidative stress (H2DCF-DA assay), and metabolic activity (MTT assay) were applied. These assays were complemented with cell counts and transmission electron microscopy. Regardless of mineral species, particles ≤ 2 µm in diameter were taken up by the cells, suggesting that particles of all mineral species came into contact and interacted with the cells. Not all particles, however, caused strong cytotoxicity: Among all assays the tectosilicates quartz and feldspar caused sporadic maximum changes of 0.8-1.2-fold compared to controls. In contrast, cytotoxicity of the clay particles was distinctly stronger and even differed between the two particle types: mica induced concentration-dependent increases in free radicals, with consistent 1.6-1.8-fold-changes at the 250 mg L(-1) concentration, and a dilated endoplasmic reticulum. Kaolin caused concentration-dependent increases in cell membrane damage, with consistent 1.3-1.6-fold increases at the 250 mg L(-1) concentration. All effects occurred in the presence or absence of 10% fetal bovine serum. Cell numbers per se were marginally affected. Results indicate that (i.) natural mineral particles can be cytotoxic to gill epithelial cells, (ii.) their cytotoxic potential differs between mineral species, with

  9. Natural mineral particles are cytotoxic to rainbow trout gill epithelial cells in vitro.

    Directory of Open Access Journals (Sweden)

    Christian Michel

    Full Text Available Worldwide increases in fluvial fine sediment are a threat to aquatic animal health. Fluvial fine sediment is always a mixture of particles whose mineralogical composition differs depending on the sediment source and catchment area geology. Nonetheless, whether particle impact in aquatic organisms differs between mineral species remains to be investigated. This study applied an in vitro approach to evaluate cytotoxicity and uptake of four common fluvial mineral particles (quartz, feldspar, mica, and kaolin; concentrations: 10, 50, 250 mg L(-1 in the rainbow trout epithelial gill cell line RTgill-W1. Cells were exposed for 24, 48, 72, and 96 h. Cytotoxicity assays for cell membrane integrity (propidium iodide assay, oxidative stress (H2DCF-DA assay, and metabolic activity (MTT assay were applied. These assays were complemented with cell counts and transmission electron microscopy. Regardless of mineral species, particles ≤ 2 µm in diameter were taken up by the cells, suggesting that particles of all mineral species came into contact and interacted with the cells. Not all particles, however, caused strong cytotoxicity: Among all assays the tectosilicates quartz and feldspar caused sporadic maximum changes of 0.8-1.2-fold compared to controls. In contrast, cytotoxicity of the clay particles was distinctly stronger and even differed between the two particle types: mica induced concentration-dependent increases in free radicals, with consistent 1.6-1.8-fold-changes at the 250 mg L(-1 concentration, and a dilated endoplasmic reticulum. Kaolin caused concentration-dependent increases in cell membrane damage, with consistent 1.3-1.6-fold increases at the 250 mg L(-1 concentration. All effects occurred in the presence or absence of 10% fetal bovine serum. Cell numbers per se were marginally affected. Results indicate that (i. natural mineral particles can be cytotoxic to gill epithelial cells, (ii. their cytotoxic potential differs between mineral

  10. Surface transport and stable trapping of particles and cells by an optical waveguide loop.

    Science.gov (United States)

    Hellesø, Olav Gaute; Løvhaugen, Pål; Subramanian, Ananth Z; Wilkinson, James S; Ahluwalia, Balpreet Singh

    2012-09-21

    Waveguide trapping has emerged as a useful technique for parallel and planar transport of particles and biological cells and can be integrated with lab-on-a-chip applications. However, particles trapped on waveguides are continuously propelled forward along the surface of the waveguide. This limits the practical usability of the waveguide trapping technique with other functions (e.g. analysis, imaging) that require particles to be stationary during diagnosis. In this paper, an optical waveguide loop with an intentional gap at the centre is proposed to hold propelled particles and cells. The waveguide acts as a conveyor belt to transport and deliver the particles/cells towards the gap. At the gap, the diverging light fields hold the particles at a fixed position. The proposed waveguide design is numerically studied and experimentally implemented. The optical forces on the particle at the gap are calculated using the finite element method. Experimentally, the method is used to transport and trap micro-particles and red blood cells at the gap with varying separations. The waveguides are only 180 nm thick and thus could be integrated with other functions on the chip, e.g. microfluidics or optical detection, to make an on-chip system for single cell analysis and to study the interaction between cells.

  11. SEPARATION OF CELL POPULATIONS BY SUPER-PARAMAGNETIC PARTICLES WITH CONTROLLED SURFACE FUNCTIONALITY

    Directory of Open Access Journals (Sweden)

    Lootsik M. D.

    2014-02-01

    Full Text Available The recognition and isolation of specific mammalian cells by the biocompatible polymer coated super-paramagnetic particles with determined surface functionality were studied. The method of synthesis of nanoscaled particles on a core of iron III oxide (Fe2O3, magemit coated with a polymer shell containing reactive oligoperoxide groups for attachment of ligands is described. By using the developed superparamagnetic particles functionalized with peanut agglutinin (PNA we have separated the sub-populations of PNA+ and PNA– cells from ascites of murine Nemeth-Kellner lymphoma. In another type of experiment, the particles were opsonized with proteins of the fetal calf serum that improved biocompatibility of the particles and their ingestion by cultivated murine macrophages J774.2. Macrophages loaded with the particles were effeciently separated from the particles free cells by using the magnet. Thus, the developed surface functionalized superparamagnetic particles showed to be a versatile tool for cell separation independent on the mode of particles’ binding with cell surface or their engulfment by the targeted cells.

  12. Development and testing of cut-cell boundaries for electromagnetic particle-in-cell codes.

    Science.gov (United States)

    Nieter, Chet; Smithe, David N.; Stoltz, Peter H.; Cary, John R.

    2007-03-01

    The finite difference time domain (FDTD) approach for electromagnetic particle-in-cell (EM-PIC) is a proven method for many problems involving interactions of charged particles with electromagnetic fields. However accurately modeling fields and particle process at complex boundaries with such methods is still an active research topic. A variety of methods have been developed for this purpose but the testing and application of these methods to real world problems in fairly limited. We have recently implemented the Dey-Mittra boundary algorithm into our EM-PIC code VORPAL. Convergence tests comparing how the frequency of cavity oscillations converge to the physical values for simulations run with stair-step and Dey-Mittra algorithms will be presented. These tests demonstrate how the Dey-Mittra algorithm provides considerable improvements over stair step boundaries. A method to correct for the image charge accumulation from removing particles at complex surfaces will also be presented. Applications to superconducting RF cavities and high-powered microwave devices will be presented.

  13. Perfluorocarbon particle size influences magnetic resonance signal and immunological properties of dendritic cells.

    Directory of Open Access Journals (Sweden)

    Helmar Waiczies

    Full Text Available The development of cellular tracking by fluorine ((19F magnetic resonance imaging (MRI has introduced a number of advantages for following immune cell therapies in vivo. These include improved signal selectivity and a possibility to correlate cells labeled with fluorine-rich particles with conventional anatomic proton ((1H imaging. While the optimization of the cellular labeling method is clearly important, the impact of labeling on cellular dynamics should be kept in mind. We show by (19F MR spectroscopy (MRS that the efficiency in labeling cells of the murine immune system (dendritic cells by perfluoro-15-crown-5-ether (PFCE particles increases with increasing particle size (560>365>245>130 nm. Dendritic cells (DC are professional antigen presenting cells and with respect to impact of PFCE particles on DC function, we observed that markers of maturation for these cells (CD80, CD86 were also significantly elevated following labeling with larger PFCE particles (560 nm. When labeled with these larger particles that also gave an optimal signal in MRS, DC presented whole antigen more robustly to CD8+ T cells than control cells. Our data suggest that increasing particle size is one important feature for optimizing cell labeling by PFCE particles, but may also present possible pitfalls such as alteration of the immunological status of these cells. Therefore depending on the clinical scenario in which the (19F-labeled cellular vaccines will be applied (cancer, autoimmune disease, transplantation, it will be interesting to monitor the fate of these cells in vivo in the relevant preclinical mouse models.

  14. Magnetic poly(lactide-co-glycolide) (PLGA) and cellulose particles for MRI-based cell tracking

    Science.gov (United States)

    Nkansah, Michael K.; Thakral, Durga; Shapiro, Erik M.

    2010-01-01

    Biodegradable, superparamagnetic micro- and nanoparticles of poly(lactide-co-glycolide) (PLGA) and cellulose were designed, fabricated and characterized for magnetic cell labeling. Monodisperse nanocrystals of magnetite were incorporated into micro- and nanoparticles of PLGA and cellulose with high efficiency using an oil-in-water single emulsion technique. Superparamagnetic cores had high magnetization (72.1 emu/g). The resulting polymeric particles had smooth surface morphology and high magnetite content (43.3 wt% for PLGA and 69.6 wt% for cellulose). While PLGA and cellulose nanoparticles displayed highest r2* values per millimole of iron (399 s-1mM-1 for cellulose and 505 s-1mM-1 for PLGA), micron-sized PLGA particles had a much higher r2* per particle than either. After incubation for a month in citrate buffer (pH 5.5), magnetic PLGA particles lost close to 50% of their initial r2* molar relaxivity, while magnetic cellulose particles remained intact, preserving over 85% of their initial r2* molar relaxivity. Lastly, mesenchymal stem cells and human breast adenocarcinoma cells were magnetically labeled using these particles with no detectable cytotoxicity. These particles are ideally suited for non-invasive cell tracking in vivo via MRI and due to their vastly different degradation properties, offer unique potential for dedicated use for either short (PLGA-based particles) or long term (cellulose-based particles) experiments. PMID:21404328

  15. Magnetic poly(lactide-co-glycolide) and cellulose particles for MRI-based cell tracking.

    Science.gov (United States)

    Nkansah, Michael K; Thakral, Durga; Shapiro, Erik M

    2011-06-01

    Biodegradable, superparamagnetic microparticles and nanoparticles of poly(lactide-co-glycolide) (PLGA) and cellulose were designed, fabricated, and characterized for magnetic cell labeling. Monodisperse nanocrystals of magnetite were incorporated into microparticles and nanoparticles of PLGA and cellulose with high efficiency using an oil-in-water single emulsion technique. Superparamagnetic cores had high magnetization (72.1 emu/g). The resulting polymeric particles had smooth surface morphology and high magnetite content (43.3 wt % for PLGA and 69.6 wt % for cellulose). While PLGA and cellulose nanoparticles displayed highest r 2* values per millimole of iron (399 sec(-1) mM(-1) for cellulose and 505 sec(-1) mM(-1) for PLGA), micron-sized PLGA particles had a much higher r 2* per particle than either. After incubation for a month in citrate buffer (pH 5.5), magnetic PLGA particles lost close to 50% of their initial r 2* molar relaxivity, while magnetic cellulose particles remained intact, preserving over 85% of their initial r 2* molar relaxivity. Lastly, mesenchymal stem cells and human breast adenocarcinoma cells were magnetically labeled using these particles with no detectable cytotoxicity. These particles are ideally suited for noninvasive cell tracking in vivo via MRI and due to their vastly different degradation properties, offer unique potential for dedicated use for either short (PLGA-based particles) or long-term (cellulose-based particles) experiments.

  16. Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes.

    Science.gov (United States)

    Ewers, Helge; Smith, Alicia E; Sbalzarini, Ivo F; Lilie, Hauke; Koumoutsakos, Petros; Helenius, Ari

    2005-10-18

    The lateral mobility of individual murine polyoma virus-like particles (VLPs) bound to live cells and artificial lipid bilayers was studied by single fluorescent particle tracking using total internal reflection fluorescence microscopy. The particle trajectories were analyzed in terms of diffusion rates and modes of motion as described by the moment scaling spectrum. Although VLPs bound to their ganglioside receptor in lipid bilayers exhibited only free diffusion, analysis of trajectories on live 3T6 mouse fibroblasts revealed three distinct modes of mobility: rapid random motion, confined movement in small zones (30-60 nm in diameter), and confined movement in zones with a slow drift. After binding to the cell surface, particles typically underwent free diffusion for 5-10 s, and then they were confined in an actin filament-dependent manner without involvement of clathrin-coated pits or caveolae. Depletion of cholesterol dramatically reduced mobility of VLPs independently of actin, whereas inhibition of tyrosine kinases had no effect on confinement. The results suggested that clustering of ganglioside molecules by the multivalent VLPs induced transmembrane coupling that led to confinement of the virus/receptor complex by cortical actin filaments.

  17. Toxicity of nano- and micro-sized ZnO particles in human lung epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Lin Weisheng [Missouri University of Science and Technology, Department of Chemistry and Environmental Research Center (United States); Xu Yi; Huang Chuanchin [Missouri University of Science and Technology, Department of Biological Sciences and Environmental Research Center (United States); Ma Yinfa [Missouri University of Science and Technology, Department of Chemistry and Environmental Research Center (United States); Shannon, Katie B. [Missouri University of Science and Technology, Department of Biological Sciences and Environmental Research Center (United States); Chen Daren [Washington University in St. Louis, Department of Energy, Environmental and Chemical Engineering (United States); Huang, Yue-Wern, E-mail: huangy@mst.ed [Missouri University of Science and Technology, Department of Biological Sciences and Environmental Research Center (United States)

    2009-01-15

    This is the first comprehensive study to evaluate the cytotoxicity, biochemical mechanisms of toxicity, and oxidative DNA damage caused by exposing human bronchoalveolar carcinoma-derived cells (A549) to 70 and 420 nm ZnO particles. Particles of either size significantly reduced cell viability in a dose- and time-dependent manner within a rather narrow dosage range. Particle mass-based dosimetry and particle-specific surface area-based dosimetry yielded two distinct patterns of cytotoxicity in both 70 and 420 nm ZnO particles. Elevated levels of reactive oxygen species (ROS) resulted in intracellular oxidative stress, lipid peroxidation, cell membrane leakage, and oxidative DNA damage. The protective effect of N-acetylcysteine on ZnO-induced cytotoxicity further implicated oxidative stress in the cytotoxicity. Free Zn{sup 2+} and metal impurities were not major contributors of ROS induction as indicated by limited free Zn{sup 2+} cytotoxicity, extent of Zn{sup 2+} dissociation in the cell culture medium, and inductively-coupled plasma-mass spectrometry metal analysis. We conclude that (1) exposure to both sizes of ZnO particles leads to dose- and time-dependent cytotoxicity reflected in oxidative stress, lipid peroxidation, cell membrane damage, and oxidative DNA damage, (2) ZnO particles exhibit a much steeper dose-response pattern unseen in other metal oxides, and (3) neither free Zn{sup 2+} nor metal impurity in the ZnO particle samples is the cause of cytotoxicity.

  18. Wave-particle interactions with parallel whistler waves: nonlinear and time-dependent effects revealed by Particle-in-Cell simulations

    NARCIS (Netherlands)

    Camporeale, E.; Zimbardo, G.

    2014-01-01

    We present self-consistent Particle-in-Cell simulations of the resonant interactions between anisotropic energetic electrons and a population of whistler waves, with parameters relevant to the Earth's radiation belt. By tracking PIC particles, and comparing with test-particles simulations we emphasi

  19. Wave-particle interactions with parallel whistler waves: nonlinear and time-dependent effects revealed by Particle-in-Cell simulations

    NARCIS (Netherlands)

    Camporeale, E.; Zimbardo, G.

    2015-01-01

    We present self-consistent Particle-in-Cell simulations of the resonant interactions between anisotropic energetic electrons and a population of whistler waves, with parameters relevant to the Earth's radiation belt. By tracking PIC particles, and comparing with test-particles simulations we emphasi

  20. Clinically viable magnetic poly(lactide-co-glycolide) (PLGA) particles for MRI-based cell tracking

    Science.gov (United States)

    Granot, Dorit; Nkansah, Michael K.; Bennewitz, Margaret F.; Tang, Kevin S.; Markakis, Eleni A.; Shapiro, Erik M.

    2013-01-01

    Purpose To design, fabricate, characterize and in vivo assay clinically viable magnetic particles for MRI-based cell tracking. Methods PLGA encapsulated magnetic nano- and microparticles were fabricated. Multiple biologically relevant experiments were performed to assess cell viability, cellular performance and stem cell differentiation. In vivo MRI experiments were performed to separately test cell transplantation and cell migration paradigms, as well as in vivo biodegradation. Results Highly magnetic nano- (~100 nm) and microparticles (~1–2 μm) were fabricated. Magnetic cell labeling in culture occurred rapidly achieving 3–50 pg Fe/cell at 3 hrs for different particles types, and >100 pg Fe/cell after 10 hours, without the requirement of a transfection agent, and with no effect on cell viability. The capability of magnetically labeled mesenchymal or neural stem cells to differentiate down multiple lineages, or for magnetically labeled immune cells to release cytokines following stimulation, was uncompromised. An in vivo biodegradation study revealed that NPs degraded ~80% over the course of 12 weeks. MRI detected as few as 10 magnetically labeled cells, transplanted into the brains of rats. Also, these particles enabled the in vivo monitoring of endogenous neural progenitor cell migration in rat brains over 2 weeks. Conclusion The robust MRI properties and benign safety profile of these particles make them promising candidates for clinical translation for MRI-based cell tracking. PMID:23568825

  1. CELL TRACKING USING PARTICLE FILTERS WITH IMPLICIT CONVEX SHAPE MODEL IN 4D CONFOCAL MICROSCOPY IMAGES

    Science.gov (United States)

    Ramesh, Nisha; Tasdizen, Tolga

    2016-01-01

    Bayesian frameworks are commonly used in tracking algorithms. An important example is the particle filter, where a stochastic motion model describes the evolution of the state, and the observation model relates the noisy measurements to the state. Particle filters have been used to track the lineage of cells. Propagating the shape model of the cell through the particle filter is beneficial for tracking. We approximate arbitrary shapes of cells with a novel implicit convex function. The importance sampling step of the particle filter is defined using the cost associated with fitting our implicit convex shape model to the observations. Our technique is capable of tracking the lineage of cells for nonmitotic stages. We validate our algorithm by tracking the lineage of retinal and lens cells in zebrafish embryos. PMID:27403085

  2. BOA, Beam Optics Analyzer A Particle-In-Cell Code

    Energy Technology Data Exchange (ETDEWEB)

    Thuc Bui

    2007-12-06

    The program was tasked with implementing time dependent analysis of charges particles into an existing finite element code with adaptive meshing, called Beam Optics Analyzer (BOA). BOA was initially funded by a DOE Phase II program to use the finite element method with adaptive meshing to track particles in unstructured meshes. It uses modern programming techniques, state-of-the-art data structures, so that new methods, features and capabilities are easily added and maintained. This Phase II program was funded to implement plasma simulations in BOA and extend its capabilities to model thermal electrons, secondary emissions, self magnetic field and implement a more comprehensive post-processing and feature-rich GUI. The program was successful in implementing thermal electrons, secondary emissions, and self magnetic field calculations. The BOA GUI was also upgraded significantly, and CCR is receiving interest from the microwave tube and semiconductor equipment industry for the code. Implementation of PIC analysis was partially successful. Computational resource requirements for modeling more than 2000 particles begin to exceed the capability of most readily available computers. Modern plasma analysis typically requires modeling of approximately 2 million particles or more. The problem is that tracking many particles in an unstructured mesh that is adapting becomes inefficient. In particular memory requirements become excessive. This probably makes particle tracking in unstructured meshes currently unfeasible with commonly available computer resources. Consequently, Calabazas Creek Research, Inc. is exploring hybrid codes where the electromagnetic fields are solved on the unstructured, adaptive mesh while particles are tracked on a fixed mesh. Efficient interpolation routines should be able to transfer information between nodes of the two meshes. If successfully developed, this could provide high accuracy and reasonable computational efficiency.

  3. Soft particle analysis of electrokinetics of biological cells and their model systems

    Directory of Open Access Journals (Sweden)

    Kimiko Makino and Hiroyuki Ohshima

    2011-01-01

    Full Text Available In this article, we review the applications of a novel theory (Ohshima 2009 Sci. Technol. Adv. Mater. 10 063001 to the analysis of electrokinetic data for various soft particles, that is, particles covered with an ion-permeable surface layer of polyelectrolytes. Soft particles discussed in this review include various biological cells and hydrogel-coated particles as a model of biological cells. Cellular transformations increase the concentration of sialic acid of glycoproteins and are associated with blocked biosynthesis of glycolipids and aberrant expression of the developmentally programmed biosynthetic pathway. The change in shape or biological function of cells may affect their surface properties and can be detected by electrokinetic measurements. The experimental results were analyzed with Ohshima's electrokinetic formula for soft particles and soft surfaces. As a model system, hydrogel surfaces that mimic biological surfaces were also prepared and their surface properties were studied.

  4. Self-propagating calciferous particles detected in a human cell line Kasumi-6 (JCRB1024).

    Science.gov (United States)

    Harasawa, Ryô; Tanabe, Hideyuki; Kurematsu, Miharu; Mizusawa, Hiroshi; Suzuki, Yoshimitsu

    2006-01-01

    Tiny particles were found in the medium in the presence of the human leukemia cell line Kasumi-6. The particles were separated from human cells by filtration and incubated in RPMI1640 supplemented with 10% fetal calf serum at 37 C. The particles increased in number very slowly in the liquid medium but did not reveal any biological activity. Transmission electron microscopy of the particles showed a spheroid or ovoid shape in ultrathin section. No specific polypeptides from the purified particles were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), except for bovine fetuin that adsorbed to the surface of the particles. X-ray diffractometry as well as Fourier transform infrared spectrometry suggested the particles consisted of hydroxyapatite. The mechanism of self-propagation of the hydroxyapatite particles in liquid medium is currently unknown. This type of particle has been overlooked for a long period because it is noncultivable. It will be necessary to examine its biological effects to the cultured cells.

  5. Wave-particle interactions with parallel whistler waves: nonlinear and time-dependent effects revealed by Particle-in-Cell simulations

    OpenAIRE

    Camporeale, Enrico; Zimbardo, G.

    2015-01-01

    We present a self-consistent Particle-in-Cell simulation of the resonant interactions between anisotropic energetic electrons and a population of whistler waves, with parameters relevant to the Earths radiation belt. By tracking PIC particles, and comparing with test-particle simulations we emphasize the importance of including nonlinear effects and time evolution in the modeling of wave-particle interactions, which are excluded in the resonant limit of quasi- linear theory routinely used in ...

  6. Titanium Dioxide Particle Type and Concentration Influence the Inflammatory Response in Caco-2 Cells.

    Science.gov (United States)

    Tada-Oikawa, Saeko; Ichihara, Gaku; Fukatsu, Hitomi; Shimanuki, Yuka; Tanaka, Natsuki; Watanabe, Eri; Suzuki, Yuka; Murakami, Masahiko; Izuoka, Kiyora; Chang, Jie; Wu, Wenting; Yamada, Yoshiji; Ichihara, Sahoko

    2016-04-16

    Titanium dioxide (TiO₂) nanoparticles are widely used in cosmetics, sunscreens, biomedicine, and food products. When used as a food additive, TiO₂ nanoparticles are used in significant amounts as white food-coloring agents. However, the effects of TiO₂ nanoparticles on the gastrointestinal tract remain unclear. The present study was designed to determine the effects of five TiO₂ particles of different crystal structures and sizes in human epithelial colorectal adenocarcinoma (Caco-2) cells and THP-1 monocyte-derived macrophages. Twenty-four-hour exposure to anatase (primary particle size: 50 and 100 nm) and rutile (50 nm) TiO₂ particles reduced cellular viability in a dose-dependent manner in THP-1 macrophages, but in not Caco-2 cells. However, 72-h exposure of Caco-2 cells to anatase (50 nm) TiO₂ particles reduced cellular viability in a dose-dependent manner. The highest dose (50 µg/mL) of anatase (100 nm), rutile (50 nm), and P25 TiO₂ particles also reduced cellular viability in Caco-2 cells. The production of reactive oxygen species tended to increase in both types of cells, irrespective of the type of TiO₂ particle. Exposure of THP-1 macrophages to 50 µg/mL of anatase (50 nm) TiO₂ particles increased interleukin (IL)-1β expression level, and exposure of Caco-2 cells to 50 µg/mL of anatase (50 nm) TiO₂ particles also increased IL-8 expression. The results indicated that anatase TiO₂ nanoparticles induced inflammatory responses compared with other TiO₂ particles. Further studies are required to determine the in vivo relevance of these findings to avoid the hazards of ingested particles.

  7. Titanium Dioxide Particle Type and Concentration Influence the Inflammatory Response in Caco-2 Cells

    Directory of Open Access Journals (Sweden)

    Saeko Tada-Oikawa

    2016-04-01

    Full Text Available Titanium dioxide (TiO2 nanoparticles are widely used in cosmetics, sunscreens, biomedicine, and food products. When used as a food additive, TiO2 nanoparticles are used in significant amounts as white food-coloring agents. However, the effects of TiO2 nanoparticles on the gastrointestinal tract remain unclear. The present study was designed to determine the effects of five TiO2 particles of different crystal structures and sizes in human epithelial colorectal adenocarcinoma (Caco-2 cells and THP-1 monocyte-derived macrophages. Twenty-four-hour exposure to anatase (primary particle size: 50 and 100 nm and rutile (50 nm TiO2 particles reduced cellular viability in a dose-dependent manner in THP-1 macrophages, but in not Caco-2 cells. However, 72-h exposure of Caco-2 cells to anatase (50 nm TiO2 particles reduced cellular viability in a dose-dependent manner. The highest dose (50 µg/mL of anatase (100 nm, rutile (50 nm, and P25 TiO2 particles also reduced cellular viability in Caco-2 cells. The production of reactive oxygen species tended to increase in both types of cells, irrespective of the type of TiO2 particle. Exposure of THP-1 macrophages to 50 µg/mL of anatase (50 nm TiO2 particles increased interleukin (IL-1β expression level, and exposure of Caco-2 cells to 50 µg/mL of anatase (50 nm TiO2 particles also increased IL-8 expression. The results indicated that anatase TiO2 nanoparticles induced inflammatory responses compared with other TiO2 particles. Further studies are required to determine the in vivo relevance of these findings to avoid the hazards of ingested particles.

  8. Enhancement of proinflammatory and procoagulant responses to silica particles by monocyte-endothelial cell interactions

    Directory of Open Access Journals (Sweden)

    Liu Xin

    2012-09-01

    Full Text Available Abstract Background Inorganic particles, such as drug carriers or contrast agents, are often introduced into the vascular system. Many key components of the in vivo vascular environment include monocyte-endothelial cell interactions, which are important in the initiation of cardiovascular disease. To better understand the effect of particles on vascular function, the present study explored the direct biological effects of particles on human umbilical vein endothelial cells (HUVECs and monocytes (THP-1 cells. In addition, the integrated effects and possible mechanism of particle-mediated monocyte-endothelial cell interactions were investigated using a coculture model of HUVECs and THP-1 cells. Fe3O4 and SiO2 particles were chosen as the test materials in the present study. Results The cell viability data from an MTS assay showed that exposure to Fe3O4 or SiO2 particles at concentrations of 200 μg/mL and above significantly decreased the cell viability of HUVECs, but no significant loss in viability was observed in the THP-1 cells. TEM images indicated that with the accumulation of SiO2 particles in the cells, the size, structure and morphology of the lysosomes significantly changed in HUVECs, whereas the lysosomes of THP-1 cells were not altered. Our results showed that reactive oxygen species (ROS generation; the production of interleukin (IL-6, IL-8, monocyte chemoattractant protein 1 (MCP-1, tumor necrosis factor (TNF-α and IL-1β; and the expression of CD106, CD62E and tissue factor in HUVECs and monocytes were significantly enhanced to a greater degree in the SiO2-particle-activated cocultures compared with the individual cell types alone. In contrast, exposure to Fe3O4 particles had no impact on the activation of monocytes or endothelial cells in monoculture or coculture. Moreover, using treatment with the supernatants of SiO2-particle-stimulated monocytes or HUVECs, we found that the enhancement of proinflammatory response by SiO2

  9. Dendritic cells enhance UHMWPE wear particle-induced osteoclast differentiation of macrophages.

    Science.gov (United States)

    Cang, Dingwei; Guo, Kaijin; Zhao, Fengchao

    2015-10-01

    Ultra-high molecular weight polyethylene (UHMWPE) has been widely used in large joint replacement. Osteolysis induced by the UHMWPE wear particles is one of the main causes of replacement failure. This study aims to elucidate whether dendritic cells play a role in UHMWPE particle-induced osteolysis. An in vitro Raw 264.7 and DC 2.4 coculture system was employed to examine the effects of dendritic cells on the inflammatory and osteoclastogenic responses of Raw 264.7 toward UHMWPE particles. The expression of cytokines, NF-κB, and osteoclast marker genes was analyzed by ELISA, western blot, or quantitative PCR. The osteoclast differentiation was measured by TRAP staining and flow cytometry. UHMWPE particles induced Raw 264.7 cells to differentiate into osteoclasts, which was enhanced by coculturing with DC 2.4 cells. DC 2.4 cells augmented UHMWPE particle-elicited activation of NF-κB signaling, higher levels of TNF-α and MCP-1, and an increased expression of MMP-9, Calcr, and Ctsk, though DC 2.4 coculture alone did not significantly cause the aforementioned changes. These results suggest that dendritic cells, among other immune cells recruited by UHMWPE particle induced inflammation, could further exacerbate inflammation and osteolysis.

  10. Macrophages detoxify the genotoxic and cytotoxic effects of surgical cobalt chrome alloy particles but not quartz particles on human cells in vitro.

    Science.gov (United States)

    Papageorgiou, I; Shadrick, V; Davis, S; Hails, L; Schins, R; Newson, R; Fisher, J; Ingham, E; Case, C P

    2008-08-25

    Particles of surgical cobalt chrome alloy are cytotoxic and genotoxic to human fibroblasts in vitro. In vivo orthopaedic patients are exposed to cobalt chrome particles as a result of wear of a joint replacement. Many of the wear debris particles that are produced are phagocytosed by macrophages that accumulate at the site of the worn implant and are disseminated to local and distant lymph nodes the liver and the spleen. In this study we have tested whether this process of phagocytosis could have altered the cytotoxic and genotoxic properties of the cobalt chrome particles. Quartz particles have been investigated as a control. Micron-sized particles of cobalt chrome alloy were internalised by either white cells of peripheral blood or by THP-1 monocytes for 1 week and 1 day, respectively. The particles were then extracted and presented at different doses to fibroblasts for 1 day. There was a reduction of the cytotoxicity and genotoxicity of the cobalt chrome particles after phagocytosis by white cells or THP-1 cells. Cobalt chrome particles that were internalised by fibroblasts also showed a reduction of their cytotoxicity but not their genotoxicity. In contrast the cytotoxicity and genotoxicity of quartz particles was increased after internalisation by THP-1 cells. The surface morphology of the cobalt chrome particles but not the quartz particles was changed after phagocytosis by THP-1 cells. This study suggests that the genotoxic and cytotoxic properties of particles that fall within the size range for phagocytosis may be highly complex in vivo and depend on the combination of material type and previous phagocytosis. These results may have relevance for particle exposure from orthopaedic implants and from environmental or industrial pollution.

  11. Effect of particle collisions and aggregation on red blood cell passage through a bifurcation.

    Science.gov (United States)

    Chesnutt, J K W; Marshall, J S

    2009-12-01

    Blood flow through bifurcating vessels in the microvasculature leads to uneven distribution of red blood cells (RBC) in the downstream channels when the channels have different sizes or the flow rates through the channels are different. This phenomenon, known as plasma skimming, is responsible for the large variation in hematocrit throughout the circulatory system. Furthermore, the strong streamline curvature present within bifurcations leads to frequent collisions between the blood elements (red and white blood cells and platelets) and the vessel walls, as well as a rearrangement of the distribution of the blood elements in the channels downstream of the bifurcation. Computational models of bifurcation flows typically neglect collision and adhesion of RBCs with each other. In this paper, we use a new type of discrete-element model to investigate the effect of particle-particle collisions and RBC aggregation on modeling of plasma skimming in bifurcations. Cases are examined with and without RBC adhesion and for different hematocrit values, including validation against previous computational results. Results show significant plasma skimming in the low-flow daughter branch and an increase in fractional particle flux with increased hematocrit, as in experimental studies. Accounting for particle-particle collisions leads to a considerable increase in collision rate of particles with the vessel wall. Particles are found to approximately follow fluid velocity streamlines, and consequently particle-particle collisions and aggregation do not significantly affect plasma skimming.

  12. A 2-D Implicit, Energy and Charge Conserving Particle In Cell Method

    Energy Technology Data Exchange (ETDEWEB)

    McPherson, Allen L. [Los Alamos National Laboratory; Knoll, Dana A. [Los Alamos National Laboratory; Cieren, Emmanuel B. [Los Alamos National Laboratory; Feltman, Nicolas [Los Alamos National Laboratory; Leibs, Christopher A. [Los Alamos National Laboratory; McCarthy, Colleen [Los Alamos National Laboratory; Murthy, Karthik S. [Los Alamos National Laboratory; Wang, Yijie [Los Alamos National Laboratory

    2012-09-10

    Recently, a fully implicit electrostatic 1D charge- and energy-conserving particle-in-cell algorithm was proposed and implemented by Chen et al ([2],[3]). Central to the algorithm is an advanced particle pusher. Particles are moved using an energy conserving scheme and are forced to stop at cell faces to conserve charge. Moreover, a time estimator is used to control errors in momentum. Here we implement and extend this advanced particle pusher to include 2D and electromagnetic fields. Derivations of all modifications made are presented in full. Special consideration is taken to ensure easy coupling into the implicit moment based method proposed by Taitano et al [19]. Focus is then given to optimizing the presented particle pusher on emerging architectures. Two multicore implementations, and one GPU (Graphics Processing Unit) implementation are discussed and analyzed.

  13. Elastic cell membranes induce long-lived anomalous thermal diffusion on nearby particles

    CERN Document Server

    Daddi-Moussa-Ider, Abdallah; Gekle, Stephan

    2016-01-01

    The physical approach of a small particle (virus, medical drug) to the cell membrane represents the crucial first step before active internalization and is governed by thermal diffusion. Using a fully analytical theory we show that the stretching and bending of the elastic membrane by the approaching particle induces a memory in the system which leads to anomalous diffusion, even though the particle is immersed in a purely Newtonian liquid. For typical cell membranes the transient subdiffusive regime extends beyond 10ms and can enhance residence times and binding rates up to 50\\%. Our analytical predictions are validated by numerical simulations.

  14. Temperature measurement of a dust particle in a RF plasma GEC reference cell

    CERN Document Server

    Kong, Jie; Matthews, Lorin S; Hyde, Truell W

    2016-01-01

    The thermal motion of a dust particle levitated in a plasma chamber is similar to that described by Brownian motion in many ways. The primary differences between a dust particle in a plasma system and a free Brownian particle is that in addition to the random collisions between the dust particle and the neutral gas atoms, there are electric field fluctuations, dust charge fluctuations, and correlated motions from the unwanted continuous signals originating within the plasma system itself. This last contribution does not include random motion and is therefore separable from the random motion in a normal temperature measurement. In this paper, we discuss how to separate random and coherent motion of a dust particle confined in a glass box in a Gaseous Electronic Conference radio frequency reference cell employing experimentally determined dust particle fluctuation data analyzed using the mean square displacement technique.

  15. An Energy- and Charge-conserving, Implicit, Electrostatic Particle-in-Cell Algorithm

    CERN Document Server

    Chen, Guangye; Barnes, Daniel C

    2011-01-01

    This paper discusses a novel fully implicit formulation for a 1D electrostatic particle-in-cell (PIC) plasma simulation approach. Unlike earlier implicit electrostatic PIC approaches (which are based on a linearized Vlasov-Poisson formulation), ours is based on a nonlinearly converged Vlasov-Amp\\`ere (VA) model. By iterating particles and fields to a tight nonlinear convergence tolerance, the approach features superior stability and accuracy properties, avoiding most of the accuracy pitfalls in earlier implicit PIC implementations. In particular, the formulation is stable against temporal (CFL) and spatial (aliasing) instabilities. It is charge- and energy-conserving to numerical roundoff for arbitrary implicit time steps. While momentum is not exactly conserved, errors are kept small by an adaptive particle sub-stepping orbit integrator, which is instrumental to prevent particle tunneling. The VA model is orbit-averaged along particle orbits to enforce an energy conservation theorem with particle sub-steppin...

  16. Preparation of hydrogel hollow particles for cell encapsulation by a method of polyester core degradation.

    Science.gov (United States)

    Rabanel, J-M; Hildgen, P

    2004-06-01

    Implantation of encapsulated cells in particles of less than 1 mm (micro-encapsulation) has been proposed as a cell synthesized bio-molecule delivery system. Encapsulation provides immuno-isolation, protecting foreign cells from host immune system while nutrients, oxygen and therapeutic products can diffuse freely across capsule walls. A new method is described for the synthesis of a new family of hollow microparticles for cell encapsulation. Unlike other micro-encapsulation methods, encapsulation in those devices will take place after capsule synthesis, by micro-injection. The microcapsules were prepared by a three-steps original procedure: first, synthesis of a core particle, followed by coating with a layer of epichlorohydrin cross-linked amylo-pectin gel and, finally, selective degradation of the core particle to create the cavity. Initial experiments make use of amylo-pectin cross-linked with trimetaphosphate as core particle material. However, selective degradation was difficult to achieve. In further essays, polyesters were used successfully for the preparation of core particles. Optimizations were carried out and the permeability and morphology of the hollow particles were investigated. The preliminary results show that the new method has the potential to become a standard procedure to obtain hydrogel hollow particles. Moreover, the permeability study seems to be in accordance with specifications for immuno-isolation.

  17. Effects of cell type and culture media on Interleukin-6 secretion in response to environmental particles.

    Science.gov (United States)

    Veranth, John M; Cutler, N Shane; Kaser, Erin G; Reilly, Christopher A; Yost, Garold S

    2008-03-01

    Cultured lung cells provide an alternative to animal exposures for comparing the effects of different types of air pollution particles. Studies of particulate matter in vitro have reported proinflammatory cytokine signaling in response to many types of environmental particles, but there have been few studies comparing identical treatments in multiple cell types or identical cells with alternative cell culture protocols. We compared soil-derived, diesel, coal fly ash, titanium dioxide, and kaolin particles along with soluble vanadium and lipopolysaccharide, applied to airway-derived cells grown in submerged culture. Cell types included A549, BEAS-2B, RAW 264.7, and primary macrophages. The cell culture models (specific combinations of cell types and culture conditions) were reproducibly different in the cytokine signaling responses to the suite of treatments. Further, Interleukin-6 (IL-6) response to the treatments changed when the same cells, BEAS-2B, were grown in KGM versus LHC-9 media or in media containing bovine serum. The effect of changing media composition was reversible over multiple changes of media type. Other variables tested included culture well size and degree of confluence. The observation that sensitivity of a cell type to environmental agonists can be manipulated by modifying culture conditions suggests a novel approach for studying biochemical mechanisms of particle toxicity.

  18. Effects of cell type and culture media on Interleukin-6 secretion in response to environmental particles

    Energy Technology Data Exchange (ETDEWEB)

    Veranth, J.M.; Cutler, N.S.; Kaser, E.G.; Reilly, C.A.; Yost, G.S. [University of Utah, Salt Lake City, UT (United States)

    2008-03-15

    Cultured lung cells provide an alternative to animal exposures for comparing the effects of different types of air pollution particles. Studies of particulate matter in vitro have reported proinflammatory cytokine signaling in response to many types of environmental particles, but there have been few studies comparing identical treatments in multiple cell types or identical cells with alternative cell culture protocols. We compared soil-derived, diesel, coal fly ash, titanium dioxide, and kaolin particles along with soluble vanadium and lipopolysaccharide, applied to airway-derived cells grown in submerged culture. Cell types included A549, BEAS-2B, RAW 264.7, and primary macrophages. The cell culture models (specific combinations of cell types and culture conditions) were reproducibly different in the cytokine signaling responses to the suite of treatments. Further, Interleukin-6 (IL-6) response to the treatments changed when the same cells, BEAS-2B, were grown in KGM versus LHC-9 media or in media containing bovine serum. The effect of changing media composition was reversible over multiple changes of media type. Other variables tested included culture well size and degree of confluence. The observation that sensitivity of a cell type to environmental agonists can be manipulated by modifying culture conditions suggests a novel approach for studying biochemical mechanisms of particle toxicity.

  19. Mutagenic Effects of a Single and an Exact Number of α Particles in Mammalian Cells

    Science.gov (United States)

    Hei, Tom K.; Wu, Li-Jun; Liu, Su-Xian; Vannais, Diane; Waldren, Charles A.; Randers-Pehrson, Gerhard

    1997-04-01

    One of the main uncertainties in risk estimation for environmental radon exposure using lung cancer data from underground miners is the extrapolation from high- to low-dose exposure where multiple traversal is extremely rare. The biological effects of a single α particle are currently unknown. Using the recently available microbeam source at the Radiological Research Accelerator Facility at Columbia University, we examined the frequencies and molecular spectrum of S1- mutants induced in human--hamster hybrid (AL) cells by either a single or an exact number of α particles. Exponentially growing cells were stained briefly with a nontoxic concentration of Hoechst dye for image analysis, and the location of individual cells was computer-monitored. The nucleus of each cell was irradiated with either 1,2,4, or 8 α particles at a linear energy transfer of 90 keV/μ m consistent with the energy spectrum of domestic radon exposure. Although single-particle traversal was only slightly cytotoxic to AL cells (survival fraction ≈ 0.82), it was highly mutagenic, and the induced mutant fraction averaged 110 mutants per 105 survivors. In addition, both toxicity and mutant induction were dose-dependent. Multiplex PCR analysis of mutant DNA showed that the proportion of mutants with multilocus deletions increased with the number of particle traversals. These data provide direct evidence that a single α particle traversing a nucleus will have a high probability of resulting in a mutation and highlight the need for radiation protection at low doses.

  20. Enhancing internalization of silica particles in myocardial cells through surface modification.

    Science.gov (United States)

    Ornelas-Soto, Nancy; Rubio-Govea, Rodrigo; Guerrero-Beltrán, Carlos E; Vázquez-Garza, Eduardo; Bernal-Ramírez, Judith; García-García, Alejandra; Oropeza-Almazán, Yuriana; García-Rivas, Gerardo; Contreras-Torres, Flavio F

    2017-10-01

    Surface modification in nanostructured mesoporous silica particles (MSNs) can significantly increase the uptake in myocardial cells. Herein, MSNs particles were synthesized and chemically functionalized to further assess their biocompatibility in rat myocardial cell line H9c2. The surface modification resulted in particles with an enhanced cellular internallization (3-fold increase) with respect to pristine particles. Apoptosis events were not evident at all, while necrosis incidence was significant only at a higher doses (>500μg/mL). In particular, the percentage of necrotic cells decrease in a statistically significant manner for the functionalized particles at lower doses than 100μg/mL. This study concludes that the proposed surface functionalization of MSNs particles does not compromise their viability on H9c2 cells, and therefore they could potentially be used for biomedical purposes. Fourier-transform infrared, Raman, TGA/DSC, N2 adsorption-desorption, and TEM techniques were used to characterize the as-prepared materials. Confocal microscopy and flow cytometry analyses were carried out to measure the histograms of cell complexity and the half maximal inhibitory concentration, respectively. Reactive oxygen species generation was accessed using assays with MitoSOX and Amplex Red fluoroprobes. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Attachment of Sulfolobus acidocaldarius cells on coal particles

    Energy Technology Data Exchange (ETDEWEB)

    Chiu-Yu Chen; Skidmore, D.R.

    1988-03-01

    Attachment of the thermophilic microorganism Sulfolobus acidocaldarius was studied on Kentucky No. 9 coal, an Ohio coal mixtures, Ohio No. 6, a European coal designated as Sulzer coal, activated carbon and iron pyrite to define the effects of initial cell density, prior acid leaching, pyrite content, and surface area on rate and extent of preleaching attachment. The results showed that the rate of preleaching attachment was so high that equilibrium was reached in less than 5 min in most cases. Attached cells increased in number with increasing initial cell density. Prior nitric acid leaching of coal reduced the extent of cell adsorption while hydrochloric acid leaching did not affect cell attachment. Some adsorption isotherms fit the Langmuir model. The specific adsorption (cells/cm/sup 3/ coal) increased with increasing surface areas measured by nitrogen adsorption. Pyrite gave the highest extent of cell attachment based on per unit surface area comparison. Adsorption isotherms of a pyrite-selective chemical adsorbate revealed that preleaching attachment of cells was affected further by altered surface properties of the coals and that the concept of selective attachment of cells on pyrite surfaces was also supported. 22 refs., 6 figs., 1 tab.

  2. SKOV-3 cell imaging by paramagnetic particles labeled with hairpin cell-penetrating peptides

    Institute of Scientific and Technical Information of China (English)

    ZHAI Xiao-hui; LIU Min; GUO Xiao-juan; WANG Si-cen; ZHANG Hong-xia; GUO You-min

    2011-01-01

    Background The hairpin cell-penetrating peptides (hCPPs) demonstrate an interesting characteristic of conditioned activation by molecules. We hypothesized that hCPPs have the potential to selectively deliver a paramagnetic gadolinium probe into the matrix metalloproteinase 2 (MMP-2) positive human ovary adenocarcinoma cell lines,SKOV-3.Methods hCPPs were synthesized and labeled with 1,4,7,10-tetraazacyclododecane-N,N',N",N'"-tetraacetic acid gadolinium (Ⅲ) (Gd-DOTA) and fluorescein isothiocyanate (FITC) by f-moc strategy using a standard solid phase peptide synthesis protocol. MMP-2 expression and activity were demonstrated by reverse transcriptase polymerase chain reaction (RT-PCR) and zymography. Internalization and location of hCPPs in SKOV-3 cells were observed by fluorescein imaging and flow cytometery. Selective delivery of Gd-DOTA in SKOV-3 cells was observed by magnetic resonance imaging (MRI) and transmission electron microscopy (TEM).Results The uptake of hCPPs by SKOV-3 cells depended on the activity of MMP-2. T1WI signals of SKOV-3 cells treated with Gd-DOTA-hCPPs suggested the uptake of Gd-DOTA-hCPPs increased in a time- (r=0.990, P <0.01) and concentration-dependent manner (r=0.964, P <0.001), but was inhibited by a MMP-2 inhibitor. Electron-dense particles observed in the cytoplasm and nucleus by transmission electron microscopy proved the intracellular penetration of gadolinium.Conclusions hCPPs can be used as an effective vector for an MRI molecular probe to assess the activity of MMP-2.

  3. Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice.

    Science.gov (United States)

    Boylan, Brendan T; Moreira, Fernando R; Carlson, Tim W; Bernard, Kristen A

    2017-02-01

    Half of the human population is at risk of infection by an arthropod-borne virus. Many of these arboviruses, such as West Nile, dengue, and Zika viruses, infect humans by way of a bite from an infected mosquito. This infectious inoculum is insect cell-derived giving the virus particles distinct qualities not present in secondary infectious virus particles produced by infected vertebrate host cells. The insect cell-derived particles differ in the glycosylation of virus structural proteins and the lipid content of the envelope, as well as their induction of cytokines. Thus, in order to accurately mimic the inoculum delivered by arthropods, arboviruses should be derived from arthropod cells. Previous studies have packaged replicon genome in mammalian cells to produce replicon particles, which undergo only one round of infection, but no studies exist packaging replicon particles in mosquito cells. Here we optimized the packaging of West Nile virus replicon genome in mosquito cells and produced replicon particles at high concentration, allowing us to mimic mosquito cell-derived viral inoculum. These particles were mature with similar genome equivalents-to-infectious units as full-length West Nile virus. We then compared the mosquito cell-derived particles to mammalian cell-derived particles in mice. Both replicon particles infected skin at the inoculation site and the draining lymph node by 3 hours post-inoculation. The mammalian cell-derived replicon particles spread from the site of inoculation to the spleen and contralateral lymph nodes significantly more than the particles derived from mosquito cells. This in vivo difference in spread of West Nile replicons in the inoculum demonstrates the importance of using arthropod cell-derived particles to model early events in arboviral infection and highlights the value of these novel arthropod cell-derived replicon particles for studying the earliest virus-host interactions for arboviruses.

  4. Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice

    Science.gov (United States)

    Boylan, Brendan T.; Moreira, Fernando R.; Carlson, Tim W.

    2017-01-01

    Half of the human population is at risk of infection by an arthropod-borne virus. Many of these arboviruses, such as West Nile, dengue, and Zika viruses, infect humans by way of a bite from an infected mosquito. This infectious inoculum is insect cell-derived giving the virus particles distinct qualities not present in secondary infectious virus particles produced by infected vertebrate host cells. The insect cell-derived particles differ in the glycosylation of virus structural proteins and the lipid content of the envelope, as well as their induction of cytokines. Thus, in order to accurately mimic the inoculum delivered by arthropods, arboviruses should be derived from arthropod cells. Previous studies have packaged replicon genome in mammalian cells to produce replicon particles, which undergo only one round of infection, but no studies exist packaging replicon particles in mosquito cells. Here we optimized the packaging of West Nile virus replicon genome in mosquito cells and produced replicon particles at high concentration, allowing us to mimic mosquito cell-derived viral inoculum. These particles were mature with similar genome equivalents-to-infectious units as full-length West Nile virus. We then compared the mosquito cell-derived particles to mammalian cell-derived particles in mice. Both replicon particles infected skin at the inoculation site and the draining lymph node by 3 hours post-inoculation. The mammalian cell-derived replicon particles spread from the site of inoculation to the spleen and contralateral lymph nodes significantly more than the particles derived from mosquito cells. This in vivo difference in spread of West Nile replicons in the inoculum demonstrates the importance of using arthropod cell-derived particles to model early events in arboviral infection and highlights the value of these novel arthropod cell-derived replicon particles for studying the earliest virus-host interactions for arboviruses. PMID:28187142

  5. Particle-based model to simulate the micromechanics of biological cells

    Science.gov (United States)

    van Liedekerke, P.; Tijskens, E.; Ramon, H.; Ghysels, P.; Samaey, G.; Roose, D.

    2010-06-01

    This paper is concerned with addressing how biological cells react to mechanical impulse. We propose a particle based model to numerically study the mechanical response of these cells with subcellular detail. The model focuses on a plant cell in which two important features are present: (1) the cell’s interior liquidlike phase inducing hydrodynamic phenomena, and (2) the cell wall, a viscoelastic solid membrane that encloses the protoplast. In this particle modeling framework, the cell fluid is modeled by a standard smoothed particle hydrodynamics (SPH) technique. For the viscoelastic solid phase (cell wall), a discrete element method (DEM) is proposed. The cell wall hydraulic conductivity (permeability) is built in through a constitutive relation in the SPH formulation. Simulations show that the SPH-DEM model is in reasonable agreement with compression experiments on an in vitro cell and with analytical models for the basic dynamical modes of a spherical liquid filled shell. We have performed simulations to explore more complex situations such as relaxation and impact, thereby considering two cell types: a stiff plant type and a soft animal-like type. Their particular behavior (force transmission) as a function of protoplasm and cell wall viscosity is discussed. We also show that the mechanics during and after cell failure can be modeled adequately. This methodology has large flexibility and opens possibilities to quantify problems dealing with the response of biological cells to mechanical impulses, e.g., impact, and the prediction of damage on a (sub)cellular scale.

  6. Size-dependent accumulation of particles in lysosomes modulates dendritic cell function through impaired antigen degradation

    Science.gov (United States)

    Seydoux, Emilie; Rothen-Rutishauser, Barbara; Nita, Izabela M; Balog, Sandor; Gazdhar, Amiq; Stumbles, Philip A; Petri-Fink, Alke; Blank, Fabian; von Garnier, Christophe

    2014-01-01

    Introduction Nanosized particles may enable therapeutic modulation of immune responses by targeting dendritic cell (DC) networks in accessible organs such as the lung. To date, however, the effects of nanoparticles on DC function and downstream immune responses remain poorly understood. Methods Bone marrow–derived DCs (BMDCs) were exposed in vitro to 20 or 1,000 nm polystyrene (PS) particles. Particle uptake kinetics, cell surface marker expression, soluble protein antigen uptake and degradation, as well as in vitro CD4+ T-cell proliferation and cytokine production were analyzed by flow cytometry. In addition, co-localization of particles within the lysosomal compartment, lysosomal permeability, and endoplasmic reticulum stress were analyzed. Results The frequency of PS particle–positive CD11c+/CD11b+ BMDCs reached an early plateau after 20 minutes and was significantly higher for 20 nm than for 1,000 nm PS particles at all time-points analyzed. PS particles did not alter cell viability or modify expression of the surface markers CD11b, CD11c, MHC class II, CD40, and CD86. Although particle exposure did not modulate antigen uptake, 20 nm PS particles decreased the capacity of BMDCs to degrade soluble antigen, without affecting their ability to induce antigen-specific CD4+ T-cell proliferation. Co-localization studies between PS particles and lysosomes using laser scanning confocal microscopy detected a significantly higher frequency of co-localized 20 nm particles as compared with their 1,000 nm counterparts. Neither size of PS particle caused lysosomal leakage, expression of endoplasmic reticulum stress gene markers, or changes in cytokines profiles. Conclusion These data indicate that although supposedly inert PS nanoparticles did not induce DC activation or alteration in CD4+ T-cell stimulating capacity, 20 nm (but not 1,000 nm) PS particles may reduce antigen degradation through interference in the lysosomal compartment. These findings emphasize the

  7. Preparation and Characterisation of ZnO/NiO Nanocomposite Particles for Solar Cell Applications

    Directory of Open Access Journals (Sweden)

    S. Kerli

    2016-01-01

    Full Text Available The mixture of ZnO and NiO effect on solar cell has been investigated. ZnO and NiO particles were produced by hydrothermal method and the produced particles were annealed at 500°C for 1 hour. Crystal structure and morphological properties of particles were examined by X-ray diffraction (XRD and scanning electron microscope (SEM. XRD measurements showed that ZnO particles have a hexagonal wurtzite structure and NiO particles have a cubic structure. SEM results show that both ZnO and NiO particles are the form of nanoparticles. Dye-sensitized solar cells were fabricated by N-719 (Ruthenium dyes and mixing ZnO/NiO particles in different ratios, 100/0, 50/50, and 0/100. It was observed that the solar cells made with ZnO have the highest performance with the efficiency of 0.542%. In addition, it was observed that when amount of NiO ratio increases in the mixture of ZnO/NiO, the efficiencies of DSSCs were observed to decrease.

  8. Implementing Flexible and Scalable Particle-in-Cell Methods for Massively Parallel Computations

    Science.gov (United States)

    Gassmoeller, R.; Bangerth, W.; Puckett, E. G.; Thieulot, C.; Heien, E. M.

    2016-12-01

    Particle-in-cell methods have a long history in modeling of mantle convection, lithospheric deformation and crustal dynamics. They are primarily used to track material information, the strain a material has undergone, the pressure-temperature history of a certain material, or the amount of volatiles or partial melt present in a region. However, their efficient parallel implementation - in particular combined with adaptive meshes - is complicated due to the complex communication and frequent reassignment of particles to cells. Consequently, many scientific software packages accomplish this efficiency by designing particle methods for a single purpose, like the advection of scalar properties that do not evolve over time (e.g., chemical heterogeneities). Design choices for particle advection, data storage, and parallel communication are then optimized for this single purpose, making the code rigid to changing requirements. Here, we present algorithms for a flexible, scalable and efficient particle-in-cell method for massively parallel finite-element codes with adaptively changing meshes. Using a modular plugin structure, we allow maximum flexibility of the generation of particles, the carried tracer properties, the advection and output algorithms, and the projection of properties to the finite-element mesh. We discuss the complexity of the these algorithms and present scaling tests ranging up to tens of thousands of cores and tens of billions of particles. We also discuss load-balancing strategies such as balanced repartitioning for particles in adaptive meshes, quantify sources of errors for the advection of particles, as well as how a proposed velocity correction can address the divergence of the velocity within a cell, and how higher-order finite elements can reduce the need for such a correction. Finally, we present whole mantle convection models as application cases, and compare our implementation to a modern advection-field approach.. We have implemented these

  9. Adaptive particle-cell algorithm for Fokker-Planck based rarefied gas flow simulations

    Science.gov (United States)

    Pfeiffer, M.; Gorji, M. H.

    2017-04-01

    Recently, the Fokker-Planck (FP) kinetic model has been devised on the basis of the Boltzmann equation (Jenny et al., 2010; Gorji et al., 2011). Particle Monte-Carlo schemes are then introduced for simulations of rarefied gas flows based on the FP kinetics. Here the particles follow independent stochastic paths and thus a spatio-temporal resolution coarser than the collisional scales becomes possible. In contrast to the direct simulation Monte-Carlo (DSMC), the computational cost is independent of the Knudsen number resulting in efficient simulations at moderate/low Knudsen flows. In order to further exploit the efficiency of the FP method, the required particle-cell resolutions should be found, and a cell refinement strategy has to be developed accordingly. In this study, an adaptive particle-cell scheme applicable to a general unstructured mesh is derived for the FP model. Virtual sub cells are introduced for the adaptive mesh refinement. Moreover a sub cell-merging algorithm is provided to honor the minimum required number of particles per cell. For assessments, the 70 degree blunted cone reentry flow (Allgre et al., 1997) is studied. Excellent agreement between the introduced adaptive FP method and DSMC is achieved.

  10. Quantitative Magnetic Separation of Particles and Cells Using Gradient Magnetic Ratcheting.

    Science.gov (United States)

    Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

    2016-04-13

    Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting, are robust but perform coarse, qualitative separations based on surface antigen expression. A quantitative magnetic separation technology is reported using high-force magnetic ratcheting over arrays of magnetically soft micropillars with gradient spacing, and the system is used to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micropillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic field. Particles with higher IOC separate and equilibrate along the miropillar array at larger pitches. A semi-analytical model is developed that predicts behavior for particles and cells. Using the system, LNCaP cells are separated based on the bound quantity of 1 μm anti-epithelial cell adhesion molecule (EpCAM) particles as a metric for expression. The ratcheting cytometry system is able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof-of-concept, EpCAM-labeled cells from patient blood are isolated with 74% purity, demonstrating potential toward a quantitative magnetic separation instrument.

  11. Passage times of confined cancer cells and deformable particles flowing through a microfluidic channel

    Science.gov (United States)

    Khan, Zeina; Kamyabi, Nabiollah; Hussain, Fazle; Vanapalli, Siva

    Circulating tumor cells, the primary cause of cancer metastasis, have to navigate through tight extracellular matrix and capillaries. Unfortunately, understanding of the hydrodynamic interactions between cells and narrow vessel walls is lacking. Using a microfluidic channel of rectangular cross-section, we investigate cell hydrodynamic behavior by measuring cell confinement, passage time through the microchannel, and excess pressure drop. Testing with highly and lowly aggressive cancer cells shows that passage time may not always be indicative of cancer cell aggressiveness as the relationship among passage time, friction and rheology is complex. Transport of deformable particles including droplets of varying viscosity and interfacial tension, as well as elastic particles of different elastic moduli, reveals that passage times depend on particle size and, contrary to prior claims, on viscosity but not on elastic modulus. We also find that particle viscosity and not modulus controls the friction force and lubrication film thickness, suggesting that cancer cell viscosity rather than elasticity controls cell transport on short time-scales.

  12. Size-Dependent Photodynamic Anticancer Activity of Biocompatible Multifunctional Magnetic Submicron Particles in Prostate Cancer Cells.

    Science.gov (United States)

    Choi, Kyong-Hoon; Nam, Ki Chang; Malkinski, Leszek; Choi, Eun Ha; Jung, Jin-Seung; Park, Bong Joo

    2016-09-06

    In this study, newly designed biocompatible multifunctional magnetic submicron particles (CoFe₂O₄-HPs-FAs) of well-defined sizes (60, 133, 245, and 335 nm) were fabricated for application as a photosensitizer delivery agent for photodynamic therapy in cancer cells. To provide selective targeting of cancer cells and destruction of cancer cell functionality, basic cobalt ferrite (CoFe₂O₄) particles were covalently bonded with a photosensitizer (PS), which comprises hematoporphyrin (HP), and folic acid (FA) molecules. The magnetic properties of the CoFe₂O₄ particles were finely adjusted by controlling the size of the primary CoFe₂O₄ nanograins, and secondary superstructured composite particles were formed by aggregation of the nanograins. The prepared CoFe₂O₄-HP-FA exhibited high water solubility, good MR-imaging capacity, and biocompatibility without any in vitro cytotoxicity. In particular, our CoFe₂O₄-HP-FA exhibited remarkable photodynamic anticancer efficiency via induction of apoptotic death in PC-3 prostate cancer cells in a particle size- and concentration-dependent manner. This size-dependent effect was determined by the specific surface area of the particles because the number of HP molecules increased with decreasing size and increasing surface area. These results indicate that our CoFe₂O₄-HP-FA may be applicable for photodynamic therapy (PDT) as a PS delivery material and a therapeutic agent for MR-imaging based PDT owing to their high saturation value for magnetization and superparamagnetism.

  13. Topical vaccination with functionalized particles targeting dendritic cells.

    Science.gov (United States)

    Baleeiro, Renato B; Wiesmüller, Karl-Heinz; Reiter, Yoran; Baude, Barbara; Dähne, Lars; Patzelt, Alexa; Lademann, Jürgen; Barbuto, José A; Walden, Peter

    2013-08-01

    Needle-free vaccination, for reasons of safety, economy, and convenience, is a central goal in vaccine development, but it also needs to meet the immunological requirements for efficient induction of prophylactic and therapeutic immune responses. Combining the principles of noninvasive delivery to dendritic cells (DCs) through skin and the immunological principles of cell-mediated immunity, we developed microparticle-based topical vaccines. We show here that the microparticles are efficient carriers for coordinated delivery of the essential vaccine constituents to DCs for cross-presentation of the antigens and stimulation of T-cell responses. When applied to the skin, the microparticles penetrate into hair follicles and target the resident DCs, the immunologically most potent cells and site for induction of efficient immune responses. The microparticle vaccine principle can be applied to different antigen formats such as peptides and proteins, or nucleic acids coding for the antigens.

  14. Acceleration of a Particle-in-Cell Code for Space Plasma Simulations with OpenACC

    Science.gov (United States)

    Peng, Ivy Bo; Markidis, Stefano; Vaivads, Andris; Vencels, Juris; Deca, Jan; Lapenta, Giovanni; Hart, Alistair; Laure, Erwin

    2015-04-01

    We simulate space plasmas with the Particle-in-cell (PIC) method that uses computational particles to mimic electrons and protons in solar wind and in Earth magnetosphere. The magnetic and electric fields are computed by solving the Maxwell's equations on a computational grid. In each PIC simulation step, there are four major phases: interpolation of fields to particles, updating the location and velocity of each particle, interpolation of particles to grids and solving the Maxwell's equations on the grid. We use the iPIC3D code, which was implemented in C++, using both MPI and OpenMP, for our case study. By November 2014, heterogeneous systems using hardware accelerators such as Graphics Processing Unit (GPUs) and the Many Integrated Core (MIC) coprocessors for high performance computing continue growth in the top 500 most powerful supercomputers world wide. Scientific applications for numerical simulations need to adapt to using accelerators to achieve portability and scalability in the coming exascale systems. In our work, we conduct a case study of using OpenACC to offload the computation intensive parts: particle mover and interpolation of particles to grids, in a massively parallel Particle-in-Cell simulation code, iPIC3D, to multi-GPU systems. We use MPI for inter-node communication for halo exchange and communicating particles. We identify the most promising parts suitable for GPUs accelerator by profiling using CrayPAT. We implemented manual deep copy to address the challenges of porting C++ classes to GPU. We document the necessary changes in the exiting algorithms to adapt for GPU computation. We present the challenges and findings as well as our methodology for porting a Particle-in-Cell code to multi-GPU systems using OpenACC. In this work, we will present the challenges, findings and our methodology of porting a Particle-in-Cell code for space applications as follows: We profile the iPIC3D code by Cray Performance Analysis Tool (CrayPAT) and identify

  15. A Multi Level Multi Domain Method for Particle In Cell Plasma Simulations

    CERN Document Server

    Innocenti, M E; Markidis, S; Beck, A; Vapirev, A

    2012-01-01

    A novel adaptive technique for electromagnetic Particle In Cell (PIC) plasma simulations is presented here. Two main issues are identified in designing adaptive techniques for PIC simulation: first, the choice of the size of the particle shape function in progressively refined grids, with the need to avoid the exertion of self-forces on particles, and, second, the necessity to comply with the strict stability constraints of the explicit PIC algorithm. The adaptive implementation presented responds to these demands with the introduction of a Multi Level Multi Domain (MLMD) system (where a cloud of self-similar domains is fully simulated with both fields and particles) and the use of an Implicit Moment PIC method as baseline algorithm for the adaptive evolution. Information is exchanged between the levels with the projection of the field information from the refined to the coarser levels and the interpolation of the boundary conditions for the refined levels from the coarser level fields. Particles are bound to...

  16. Elaborate calibration procedure for cell irradiation at the CAS-LIBB single-particle microbeam

    Institute of Scientific and Technical Information of China (English)

    Hu Zhi-Wen; Ding Ke-Jian; Yu Liang-Deng; Zhang Jun; Wu Li-Jun; Yu Zeng-Liang

    2006-01-01

    Single-particle microbeam is uniquely capable of precisely delivering a preset number of charged particles to individual cells or sub-cellular targets to be determined in vitro.It is crucial to find a reference point that relates the microbeam's location to the microscope's plane,and align individual targets at this reference point for cell irradiation.To choose an appropriate reference point,an approach based on analysing the intensity distribution of fluorescence in a thin scintillator excited by traversing particles is newly developed using the CAS-LIBB single-particle microbeam,which features decisive physical signification and sufficient resolution.As its bonus,this on-line analysis provides precise and fast response to the determination of beam profile and potentially optimizes the microbeam quality by further adjusting hardware setup.

  17. Geometric Integration Of The Vlasov-Maxwell System With A Variational Particle-in-cell Scheme

    Energy Technology Data Exchange (ETDEWEB)

    J. Squire, H. Qin and W.M. Tang

    2012-03-27

    A fully variational, unstructured, electromagnetic particle-in-cell integrator is developed for integration of the Vlasov-Maxwell equations. Using the formalism of Discrete Exterior Calculus [1], the field solver, interpolation scheme and particle advance algorithm are derived through minimization of a single discrete field theory action. As a consequence of ensuring that the action is invariant under discrete electromagnetic gauge transformations, the integrator exactly conserves Gauss's law.

  18. Geometric integration of the Vlasov-Maxwell system with a variational particle-in-cell scheme

    Energy Technology Data Exchange (ETDEWEB)

    Squire, J.; Tang, W. M. [Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Qin, H. [Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2012-08-15

    A fully variational, unstructured, electromagnetic particle-in-cell integrator is developed for integration of the Vlasov-Maxwell equations. Using the formalism of discrete exterior calculus [Desbrun et al., e-print arXiv:math/0508341 (2005)], the field solver, interpolation scheme, and particle advance algorithm are derived through minimization of a single discrete field theory action. As a consequence of ensuring that the action is invariant under discrete electromagnetic gauge transformations, the integrator exactly conserves Gauss's law.

  19. Geometric integration of the Vlasov-Maxwell system with a variational particle-in-cell scheme

    OpenAIRE

    2014-01-01

    A fully variational, unstructured, electromagnetic particle-in-cell integrator is developed for integration of the Vlasov-Maxwell equations. Using the formalism of Discrete Exterior Calculus, the field solver, interpolation scheme and particle advance algorithm are derived through minimization of a single discrete field theory action. As a consequence of ensuring that the action is invariant under discrete electromagnetic gauge transformations, the integrator exactly conserves Gauss's law.

  20. Toxic effects of brake wear particles on epithelial lung cells in vitro

    Directory of Open Access Journals (Sweden)

    Perrenoud Alain

    2009-11-01

    Full Text Available Abstract Background Fine particulate matter originating from traffic correlates with increased morbidity and mortality. An important source of traffic particles is brake wear of cars which contributes up to 20% of the total traffic emissions. The aim of this study was to evaluate potential toxicological effects of human epithelial lung cells exposed to freshly generated brake wear particles. Results An exposure box was mounted around a car's braking system. Lung cells cultured at the air-liquid interface were then exposed to particles emitted from two typical braking behaviours („full stop“ and „normal deceleration“. The particle size distribution as well as the brake emission components like metals and carbons was measured on-line, and the particles deposited on grids for transmission electron microscopy were counted. The tight junction arrangement was observed by laser scanning microscopy. Cellular responses were assessed by measurement of lactate dehydrogenase (cytotoxicity, by investigating the production of reactive oxidative species and the release of the pro-inflammatory mediator interleukin-8. The tight junction protein occludin density decreased significantly (p Conclusion These findings suggest that the metals on brake wear particles damage tight junctions with a mechanism involving oxidative stress. Brake wear particles also increase pro-inflammatory responses. However, this might be due to another mechanism than via oxidative stress.

  1. A new charge conservation method in electromagnetic particle-in-cell simulations

    Science.gov (United States)

    Umeda, T.; Omura, Y.; Tominaga, T.; Matsumoto, H.

    2003-12-01

    We developed a fast algorithm for solving the current density satisfying the continuity equation of charge in electromagnetic particle-in-cell (PIC) simulations. In PIC simulations of the charge conservation, a particle trajectory over one time step is conventionally assumed to be a straight line. In the present new scheme we assume that a particle trajectory is a zigzag line. Compared with the Villasenor-Buneman method and Esirkepov's method, the present scheme has an advantage in computation speed without any substantial distortion of physics.

  2. Particle-in-Cell Laser-Plasma Simulation on Xeon Phi Coprocessors

    CERN Document Server

    Surmin, I A; Efimenko, E S; Gonoskov, A A; Korzhimanov, A V; Meyerov, I B

    2015-01-01

    This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss suitability of the method for Xeon Phi architecture and present our experience of porting and optimization of the existing parallel Particle-in-Cell code PICADOR. Direct porting with no code modification gives performance on Xeon Phi close to 8-core CPU on a benchmark problem with 50 particles per cell. We demonstrate step-by-step application of optimization techniques such as improving data locality, enhancing parallelization efficiency and vectorization that leads to 3.75 x speedup on CPU and 7.5 x on Xeon Phi. The optimized version achieves 18.8 ns per particle update on Intel Xeon E5-2660 CPU and 9.3 ns per particle update on Intel Xeon Phi 5110P. On a real problem of laser ion acceleration in targets with surface grating that requires a large number of macroparticles per cell the speedup of Xeon Phi compared to CPU is 1.6 x.

  3. Wear particles generated from studded tires and pavement induces inflammatory reactions in mouse macrophage cells.

    Science.gov (United States)

    Lindbom, John; Gustafsson, Mats; Blomqvist, Göran; Dahl, Andreas; Gudmundsson, Anders; Swietlicki, Erik; Ljungman, Anders G

    2007-06-01

    Health risks associated with exposure to airborne particulate matter (PM) have been shown epidemiologically as well as experimentally, pointing to both respiratory and cardiovascular effects. These health risks are of increasing concern in society, and to protect public health, a clarification of the toxic properties of particles from different sources is of importance. Lately, wear particles generated from traffic have been recognized as a major contributing source to the overall particle load, especially in the Nordic countries where studded tires are used. The aim of this study was to further investigate and compare the ability to induce inflammatory mediators of different traffic-related wear particles collected from an urban street, a subway station, and studded tire-pavement wear. Inflammatory effects were measured as induction of nitric oxide (NO), IL-6, TNF-alpha, arachidonic acid (AA), and lipid peroxidation after exposure of the murine macrophage like cell line RAW 264.7. In addition, the redox potential of the particles was measured in a cell-free system. The results show that all particles tested induce IL-6, TNF-alpha, and NO, and those from the urban street were the most potent ones. In contrast, particles collected from a subway station were most potent to induce lipid peroxidation, AA release, and formation of ROS. Particles from studded tire-pavement wear, generated using a road simulator, were able to induce inflammatory cytokines, NO, lipid peroxidation, and ROS formation. Interestingly, particles generated from pavement containing granite as the main stone material were more potent than those generated from pavement containing quartzite as the main stone material.

  4. Stochastic particle barcoding for single-cell tracking and multiparametric analysis.

    Science.gov (United States)

    Castellarnau, M; Szeto, G L; Su, H-W; Tokatlian, T; Love, J C; Irvine, D J; Voldman, J

    2015-01-27

    This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co-encapsulated within an enzymatically-degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single-cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re-identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.

  5. Induction of a bystander mutagenic effect of alpha particles in mammalian cells

    Science.gov (United States)

    Zhou, H.; Randers-Pehrson, G.; Waldren, C. A.; Vannais, D.; Hall, E. J.; Hei, T. K.; Chatterjee, A. (Principal Investigator)

    2000-01-01

    Ever since the discovery of X-rays was made by Rontgen more than a hundred years ago, it has always been accepted that the deleterious effects of ionizing radiation such as mutation and carcinogenesis are attributable mainly to direct damage to DNA. Although evidence based on microdosimetric estimation in support of a bystander effect appears to be consistent, direct proof of such extranuclear/extracellular effects are limited. Using a precision charged particle microbeam, we show here that irradiation of 20% of randomly selected A(L) cells with 20 alpha particles each results in a mutant fraction that is 3-fold higher than expected, assuming no bystander modulation effect. Furthermore, analysis by multiplex PCR shows that the types of mutants induced are significantly different from those of spontaneous origin. Pretreatment of cells with the radical scavenger DMSO had no effect on the mutagenic incidence. In contrast, cells pretreated with a 40 microM dose of lindane, which inhibits cell-cell communication, significantly decreased the mutant yield. The doses of DMSO and lindane used in these experiments are nontoxic and nonmutagenic. We further examined the mutagenic yield when 5-10% of randomly selected cells were irradiated with 20 alpha particles each. Results showed, likewise, a higher mutant yield than expected assuming no bystander effects. Our studies provide clear evidence that irradiated cells can induce a bystander mutagenic response in neighboring cells not directly traversed by alpha particles and that cell-cell communication process play a critical role in mediating the bystander phenomenon.

  6. Infected dendritic cells are sufficient to mediate the adjuvant activity generated by Venezuelan equine encephalitis virus replicon particles

    OpenAIRE

    Tonkin, Daniel R.; Whitmore, Alan; Robert E Johnston; Barro, Mario

    2012-01-01

    Replicon particles derived from Venezuelan equine encephalitis virus (VEE) are infectious non-propagating particles which act as a safe and potent systemic, mucosal, and cellular adjuvant when delivered with antigen. VEE and VEE replicon particles (VRP) can target multiple cell types including dendritic cells (DCs). The role of these cell types in VRP adjuvant activity has not been previously evaluated, and for these studies we focused on the contribution of DCs to the response to VRP. By ana...

  7. Infected dendritic cells are sufficient to mediate the adjuvant activity generated by Venezuelan equine encephalitis virus replicon particles

    OpenAIRE

    Tonkin, Daniel R.; Whitmore, Alan; Johnston, Robert E.; Barro,Mario

    2012-01-01

    Replicon particles derived from Venezuelan equine encephalitis virus (VEE) are infectious non-propagating particles which act as a safe and potent systemic, mucosal, and cellular adjuvant when delivered with antigen. VEE and VEE replicon particles (VRP) can target multiple cell types including dendritic cells (DCs). The role of these cell types in VRP adjuvant activity has not been previously evaluated, and for these studies we focused on the contribution of DCs to the response to VRP. By ana...

  8. Size-dependent accumulation of particles in lysosomes modulates dendritic cell function through impaired antigen degradation

    Directory of Open Access Journals (Sweden)

    Seydoux E

    2014-08-01

    Full Text Available Emilie Seydoux,1,2 Barbara Rothen-Rutishauser,1,3 Izabela M Nita,1 Sandor Balog,3 Amiq Gazdhar,1 Philip A Stumbles,4,5 Alke Petri-Fink,3,6 Fabian Blank,1,* Christophe von Garnier1,*1Department of Respiratory Medicine, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, 2Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland; 3Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland; 4School of Veterinary and Life Sciences, Molecular and Biomedical Sciences, Murdoch University, Perth, WA, Australia; 5Telethon Kids Institute, Perth, WA, Australia; 6Department of Chemistry, University of Fribourg, Fribourg, Switzerland*These authors contributed equally to the manuscriptIntroduction: Nanosized particles may enable therapeutic modulation of immune responses by targeting dendritic cell (DC networks in accessible organs such as the lung. To date, however, the effects of nanoparticles on DC function and downstream immune responses remain poorly understood. Methods: Bone marrow–derived DCs (BMDCs were exposed in vitro to 20 or 1,000 nm polystyrene (PS particles. Particle uptake kinetics, cell surface marker expression, soluble protein antigen uptake and degradation, as well as in vitro CD4+ T-cell proliferation and cytokine production were analyzed by flow cytometry. In addition, co-localization of particles within the lysosomal compartment, lysosomal permeability, and endoplasmic reticulum stress were analyzed. Results: The frequency of PS particle–positive CD11c+/CD11b+ BMDCs reached an early plateau after 20 minutes and was significantly higher for 20 nm than for 1,000 nm PS particles at all time-points analyzed. PS particles did not alter cell viability or modify expression of the surface markers CD11b, CD11c, MHC class II, CD40, and CD86. Although particle exposure did not modulate antigen uptake, 20 nm PS particles decreased the capacity

  9. Mutagenic effects of a single and an exact number of alpha particles in mammalian cells

    Science.gov (United States)

    Hei, T. K.; Wu, L. J.; Liu, S. X.; Vannais, D.; Waldren, C. A.; Randers-Pehrson, G.

    1997-01-01

    One of the main uncertainties in risk estimation for environmental radon exposure using lung cancer data from underground miners is the extrapolation from high- to low-dose exposure where multiple traversal is extremely rare. The biological effects of a single alpha particle are currently unknown. Using the recently available microbeam source at the Radiological Research Accelerator Facility at Columbia University, we examined the frequencies and molecular spectrum of S1- mutants induced in human-hamster hybrid (A(L)) cells by either a single or an exact number of alpha particles. Exponentially growing cells were stained briefly with a nontoxic concentration of Hoechst dye for image analysis, and the location of individual cells was computer-monitored. The nucleus of each cell was irradiated with either 1,2,4, or 8 alpha particles at a linear energy transfer of 90 keV/microm consistent with the energy spectrum of domestic radon exposure. Although single-particle traversal was only slightly cytotoxic to A(L) cells (survival fraction approximately 0.82), it was highly mutagenic, and the induced mutant fraction averaged 110 mutants per 10(5) survivors. In addition, both toxicity and mutant induction were dose-dependent. Multiplex PCR analysis of mutant DNA showed that the proportion of mutants with multilocus deletions increased with the number of particle traversals. These data provide direct evidence that a single a particle traversing a nucleus will have a high probability of resulting in a mutation and highlight the need for radiation protection at low doses.

  10. Fabrication of uniform multi-compartment particles using microfludic electrospray technology for cell co-culture studies.

    Science.gov (United States)

    Liu, Zhou; Shum, Ho Cheung

    2013-01-01

    In this work, we demonstrate a robust and reliable approach to fabricate multi-compartment particles for cell co-culture studies. By taking advantage of the laminar flow within our microfluidic nozzle, multiple parallel streams of liquids flow towards the nozzle without significant mixing. Afterwards, the multiple parallel streams merge into a single stream, which is sprayed into air, forming monodisperse droplets under an electric field with a high field strength. The resultant multi-compartment droplets are subsequently cross-linked in a calcium chloride solution to form calcium alginate micro-particles with multiple compartments. Each compartment of the particles can be used for encapsulating different types of cells or biological cell factors. These hydrogel particles with cross-linked alginate chains show similarity in the physical and mechanical environment as the extracellular matrix of biological cells. Thus, the multi-compartment particles provide a promising platform for cell studies and co-culture of different cells. In our study, cells are encapsulated in the multi-compartment particles and the viability of cells is quantified using a fluorescence microscope after the cells are stained for a live/dead assay. The high cell viability after encapsulation indicates the cytocompatibility and feasibility of our technique. Our multi-compartment particles have great potential as a platform for studying cell-cell interactions as well as interactions of cells with extracellular factors.

  11. Load-balancing techniques for a parallel electromagnetic particle-in-cell code

    Energy Technology Data Exchange (ETDEWEB)

    PLIMPTON,STEVEN J.; SEIDEL,DAVID B.; PASIK,MICHAEL F.; COATS,REBECCA S.

    2000-01-01

    QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER.

  12. No requirement of HCV 5'NCR for HCV-like particles assembly in insect cells

    Institute of Scientific and Technical Information of China (English)

    Wei Zhao; Guo-Yang Liao; Yah-Jun Jiang; Shu-De Jiang

    2003-01-01

    AIM: To express all three HCV structural proteins in the presence or absence of HCV 5'NCR to investigate the requirement of 5'NCR for the assembly of HCV-like particles in insect cells.METHODS: HCV structural protein encoding sequences CE1E2 and 5'NCR-CE1E2 were amplified with PCR.Recombinant baculovirus were constructed with recombinant DNA techniques. HCV structural proteins expressed in insect cells were analyzed by immunofluorescence and SDS-PAGE.Immunoprecipitation experiment of insect cell lysates with anti-E2 monodonal antibody (Mab) was carried out and the immunoprecipitated proteins were subjected to SDS-PAGE and immunoblotting with anti-C, anti-E2 Mabs and HCV positive serum. The virus-like particles in insect cells were visualized by electron microscopy (EM). The HCV-like particles were purified by sucrose gradient centrifugation and identified by EM and immune aggregation EM.RESULTS: The recombinant baculovirus reBV/CE1E2containing HCV C, E1, E2 genes and reBV/CS containing the same structural protein genes plus 5'NCR were constructed. The insect cells infected with either reBV/CE1E2or reBV/CS expressed HCV C, E1 and E2 proteins with a molecular weight of 20 kD, 35 kD and 66 kD respectively.The results of immunoprecipitation and the immunoblotting revealed the coimmunoprecipitation of C, E1, and E2proteins, indicating the interaction of HCV structural proteins expressed in insect cells. Electron microscopy of insect cells infected with reBV/CE1E2 or reBV/CS demonstrated spherical particles (40 to 60 nm in diameter)similar to the HCV virions from sera or hepatic tissues of HCV infected humans. The HCV-like particles were partially purified by sucrose gradient centrifugation, and the purified VLPs showed immuno-reactivity with anti-HCV antibodies.CONCLUSION: HCV 5'NCR is not required for the assembly of HCV-like particles in insect cells, HCV core and envelope proteins are sufficient for viral particle formation.

  13. Numerical Simulation of Viscous Flow Through Spherical Particle Assemblage with the Modified Cell Model

    Institute of Scientific and Technical Information of China (English)

    毛在砂

    2002-01-01

    The cell model developed since 1950s is a useful tool for exploring the behavior of particle assemblages,but it demands further careful development of the outer cell boundary conditions so that interaction in a particleswarm is better represented. In this paper, the cell model and its development were reviewed, and the modificationsof outer cell boundary conditions were suggested. At the cell outer boundary, the restriction of uniform liquid flowwas removed in our simulation conducted in the reference frame fixed with the particle. Zero shear stress conditionwas used to evaluate the outer boundary value of the stream function. Boundary vorticity was allowed to evolve tovalues compatible to existing stream function at the free shear outer boundary. The fore-aft symmetry of vorticitydistribution at the outer boundary is thought critical to ensure the continuity of inflow and outflow between touchingneighbor cells, and is also tested in the modified cell model. Numerical simulation in terms of stream function andvorticity based on the modified cell models was carried out to shed light on the interaction between liquid andparticles. Lower predicted drag coefficient by the modified cell models was interpreted with the feature of flowstructure. The drag coefficient from the simulation was also compared with correlations of drag coefficient reportedin literature. It is found that the modified cell model with the uniformity of external flow relaxed and the fore-aftsymmetry of boundary vorticity enforced was the most satisfactory on the overall performance of prediction.

  14. Pulmonary cystic keratinizing squamous cell lesions of rats after inhalation/instillation of different particles.

    Science.gov (United States)

    Rittinghausen, S; Mohr, U; Dungworth, D L

    1997-12-01

    Cystic keratinizing squamous cell lesions from three inhalation studies (Study A, B, C) and one intratracheal instillation study (Study D) in rats were reclassified and a certain number of lesions examined immunohistochemically for PCNA (proliferating cell nuclear antigen) as a marker of cellular proliferation. The following classification was used: squamous cell metaplasia with marked keratinization, keratinizing cyst, cystic keratinizing epithelioma, cystic keratinizing squamous cell carcinoma, keratinizing squamous cell carcinoma and non-keratinizing squamous cell carcinoma. In study A (inhalation of coal oven exhaust and subcutaneous injection of a high dose of DB (ah)A) 49.3% of rats developed cystic keratinizing squamous cell carcinomas. Inhalation of coal oven exhaust gas together with intratracheal instillation of crocidolite or subcutaneous injection of a low dose DB(ah)A (dibenz(ah)anthracene) resulted in cystic keratinizing squamous cell carcinomas in 23% to 24% of the rats. High incidences of cystic squamous cell carcinomas in the range of 31.9% to 76.4% were observed in rats of Study B1 after a 10-months exposure to tar/pitch condensation aerosol (different B(a)P (benzo(a)pyrene) concentrations) with added carbon black in some groups. After a 20-months exposure period to the same inhalation atmospheres (Study B2) the incidence of squamous cell carcinomas was increased up to 95.8%. Exposure of rats to various concentrations of unfiltered diesel exhaust (Study C) resulted in incidences of cystic keratinizing epitheliomas ranging from 2.5% (2.5 mg/m3) to 10.7% (7.5 mg/m3). Epitheliomas were also observed in 16.2% of carbon black and 16.0% of titanium dioxide exposed rats. Only a few cystic keratinizing squamous cell carcinomas occurred. In the intratrachel instillation study (Study D) increased incidences of cystic keratinizing epitheliomas occurred in rats exposed to native diesel exhaust particles (16.7%), high dose of extracted diesel exhaust particles

  15. Numerical prediction of algae cell mixing feature in raceway ponds using particle tracing methods.

    Science.gov (United States)

    Ali, Haider; Cheema, Taqi A; Yoon, Ho-Sung; Do, Younghae; Park, Cheol W

    2015-02-01

    In the present study, a novel technique, which involves numerical computation of the mixing length of algae particles in raceway ponds, was used to evaluate the mixing process. A value of mixing length that is higher than the maximum streamwise distance (MSD) of algae cells indicates that the cells experienced an adequate turbulent mixing in the pond. A coupling methodology was adapted to map the pulsating effects of a 2D paddle wheel on a 3D raceway pond in this study. The turbulent mixing was examined based on the computations of mixing length, residence time, and algae cell distribution in the pond. The results revealed that the use of particle tracing methodology is an improved approach to define the mixing phenomenon more effectively. Moreover, the algae cell distribution aided in identifying the degree of mixing in terms of mixing length and residence time.

  16. Micro-particle transporting system using galvanotactically stimulated apo-symbiotic cells of Paramecium bursaria.

    Science.gov (United States)

    Furukawa, Shunsuke; Karaki, Chiaki; Kawano, Tomonori

    2009-01-01

    It is well known that Paramecium species including green paramecia (Paramecium bursaria) migrate towards the anode when exposed to an electric field in a medium. This type of a cellular movement is known as galvanotaxis. Our previous study revealed that an electric stimulus given to P bursaria is converted to a galvanotactic cellular movement by involvement of T-type calcium channel on the plasma membrane [Aonuma et al. (2007), Z. Naturforsch. 62c, 93-102]. This phenomenon has attracted the attention of bioengineers in the fields of biorobotics or micro-robotics in order to develop electrically controllable micromachineries. Here, we demonstrate the galvanotactic controls of the cellular migration of P bursaria in capillary tubes (diameter, 1-2 mm; length, 30-240 mm). Since the Paramecium cells take up particles of various sizes, we attempted to use the electrically stimulated cells of P bursaria as the vehicle for transportation of micro-particles in the capillary system. By using apo-symbiotic cells of P bursaria obtained after forced removal of symbiotic algae, the uptake of the particles could be maximized and visualized. Then, electrically controlled transportations of particle-filled apo-symbiotic P bursaria cells were manifested. The particles transported by electrically controlled cells (varying in size from nm to /m levels) included re-introduced green algae, fluorescence-labeled polystyrene beads, magnetic microspheres, emerald green fluorescent protein (EmGFP)-labeled cells of E. coli, Indian ink, and crystals of zeolite (hydrated aluminosilicate minerals with a micro-porous structure) and some metal oxides. Since the above demonstrations were successful, we concluded that P bursaria has a potential to be employed as one of the micro-biorobotic devices used in BioMEMS (biological micro-electro-mechanical systems).

  17. Effects of nano-scaled particles on endothelial cell function in vitro: studies on viability, proliferation and inflammation.

    Science.gov (United States)

    Peters, Kirsten; Unger, Ronald E; Kirkpatrick, C James; Gatti, Antonietta M; Monari, Emanuela

    2004-04-01

    Recent studies give support for a connection between the presence of inorganic particles (of microm and nm size) in different organs and tissues and the development of inflammatory foci, called granulomas. As the potential source of particles (e.g. porcelain dental bridges) and the location of particle detection were topographically far apart, a distribution via the blood stream appears highly probable. Thus, endothelial cells, which line the inner surface of blood vessels, would come into direct contact with these particles, making particle-endothelial interactions potentially pathogenically relevant. The objective of this study was to evaluate the effects that five different nano-scaled particles (PVC, TiO2, SiO2, Co, Ni) have on endothelial cell function and viability. Therefore, human endothelial cells were exposed to different amounts of the above-mentioned particles. Although most particle types are shown to be internalised (except Ni-particles), only Co-particles possessed cytotoxic effects. Furthermore, an impairment of the proliferative activity and a pro-inflammatory stimulation of endothelial cells were induced by exposure to Co- and, to a lesser extent, by SiO2-particles. If a pro-inflammatory stimulation of endothelial cells occurs in vivo, a chronic inflammation could be a possible consequence.

  18. An energy- and charge-conserving, implicit, electrostatic particle-in-cell algorithm

    Science.gov (United States)

    Chen, G.; Chacón, L.; Barnes, D. C.

    2011-08-01

    This paper discusses a novel fully implicit formulation for a one-dimensional electrostatic particle-in-cell (PIC) plasma simulation approach. Unlike earlier implicit electrostatic PIC approaches (which are based on a linearized Vlasov-Poisson formulation), ours is based on a nonlinearly converged Vlasov-Ampére (VA) model. By iterating particles and fields to a tight nonlinear convergence tolerance, the approach features superior stability and accuracy properties, avoiding most of the accuracy pitfalls in earlier implicit PIC implementations. In particular, the formulation is stable against temporal (Courant-Friedrichs-Lewy) and spatial (aliasing) instabilities. It is charge- and energy-conserving to numerical round-off for arbitrary implicit time steps (unlike the earlier "energy-conserving" explicit PIC formulation, which only conserves energy in the limit of arbitrarily small time steps). While momentum is not exactly conserved, errors are kept small by an adaptive particle sub-stepping orbit integrator, which is instrumental to prevent particle tunneling (a deleterious effect for long-term accuracy). The VA model is orbit-averaged along particle orbits to enforce an energy conservation theorem with particle sub-stepping. As a result, very large time steps, constrained only by the dynamical time scale of interest, are possible without accuracy loss. Algorithmically, the approach features a Jacobian-free Newton-Krylov solver. A main development in this study is the nonlinear elimination of the new-time particle variables (positions and velocities). Such nonlinear elimination, which we term particle enslavement, results in a nonlinear formulation with memory requirements comparable to those of a fluid computation, and affords us substantial freedom in regards to the particle orbit integrator. Numerical examples are presented that demonstrate the advertised properties of the scheme. In particular, long-time ion acoustic wave simulations show that numerical

  19. Engineering tubular bone using mesenchymal stem cell sheets and coral particles

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Wenxin [Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, No.229 North Taibai Road, Xi’an 710069 (China); Ma, Dongyang [Department of Oral and Maxillofacial Surgery, Lanzhou General Hospital, Lanzhou Command of PLA, BinHe 333 South Road, Lanzhou 730052 (China); Yan, Xingrong; Liu, Liangqi; Cui, Jihong; Xie, Xin; Li, Hongmin [Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, No.229 North Taibai Road, Xi’an 710069 (China); Chen, Fulin, E-mail: chenfl@nwu.edu.cn [Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, No.229 North Taibai Road, Xi’an 710069 (China)

    2013-04-19

    Highlights: • We developed a novel engineering strategy to solve the limitations of bone grafts. • We fabricated tubular constructs using cell sheets and coral particles. • The composite constructs showed high radiological density and compressive strength. • These characteristics were similar to those of native bone. -- Abstract: The development of bone tissue engineering has provided new solutions for bone defects. However, the cell-scaffold-based approaches currently in use have several limitations, including low cell seeding rates and poor bone formation capacity. In the present study, we developed a novel strategy to engineer bone grafts using mesenchymal stem cell sheets and coral particles. Rabbit bone marrow mesenchymal stem cells were continuously cultured to form a cell sheet with osteogenic potential and coral particles were integrated into the sheet. The composite sheet was then wrapped around a cylindrical mandrel to fabricate a tubular construct. The resultant tubular construct was cultured in a spinner-flask bioreactor and subsequently implanted into a subcutaneous pocket in a nude mouse for assessment of its histological characteristics, radiological density and mechanical property. A similar construct assembled from a cell sheet alone acted as a control. In vitro observations demonstrated that the composite construct maintained its tubular shape, and exhibited higher radiological density, compressive strength and greater extracellular matrix deposition than did the control construct. In vivo experiments further revealed that new bone formed ectopically on the composite constructs, so that the 8-week explants of the composite sheets displayed radiological density similar to that of native bone. These results indicate that the strategy of using a combination of a cell sheet and coral particles has great potential for bone tissue engineering and repairing bone defects.

  20. Size-Dependent Photodynamic Anticancer Activity of Biocompatible Multifunctional Magnetic Submicron Particles in Prostate Cancer Cells

    Directory of Open Access Journals (Sweden)

    Kyong-Hoon Choi

    2016-09-01

    Full Text Available In this study, newly designed biocompatible multifunctional magnetic submicron particles (CoFe2O4-HPs-FAs of well-defined sizes (60, 133, 245, and 335 nm were fabricated for application as a photosensitizer delivery agent for photodynamic therapy in cancer cells. To provide selective targeting of cancer cells and destruction of cancer cell functionality, basic cobalt ferrite (CoFe2O4 particles were covalently bonded with a photosensitizer (PS, which comprises hematoporphyrin (HP, and folic acid (FA molecules. The magnetic properties of the CoFe2O4 particles were finely adjusted by controlling the size of the primary CoFe2O4 nanograins, and secondary superstructured composite particles were formed by aggregation of the nanograins. The prepared CoFe2O4-HP-FA exhibited high water solubility, good MR-imaging capacity, and biocompatibility without any in vitro cytotoxicity. In particular, our CoFe2O4-HP-FA exhibited remarkable photodynamic anticancer efficiency via induction of apoptotic death in PC-3 prostate cancer cells in a particle size- and concentration-dependent manner. This size-dependent effect was determined by the specific surface area of the particles because the number of HP molecules increased with decreasing size and increasing surface area. These results indicate that our CoFe2O4-HP-FA may be applicable for photodynamic therapy (PDT as a PS delivery material and a therapeutic agent for MR-imaging based PDT owing to their high saturation value for magnetization and superparamagnetism.

  1. Radiobiological Effects of Alpha-Particles from Astatine-211: From DNA Damage to Cell Death

    Energy Technology Data Exchange (ETDEWEB)

    Claesson, Kristina

    2011-05-15

    In recent years, the use of high linear energy transfer (LET) radiation for radiotherapeutic applications has gained increased interest. Astatine-211 (211At) is an alpha-particle emitting radionuclide, promising for targeted radioimmunotherapy of isolated tumor cells and microscopic clusters. To improve development of safe radiotherapy using 211At it is important to increase our knowledge of the radiobiological effects in cells. During radiotherapy, both tumors and adjacent normal tissue will be irradiated and therefore, it is of importance to understand differences in the radio response between proliferating and resting cells. The aim of this thesis was to investigate effects in fibroblasts with different proliferation status after irradiation with alpha-particles from 211At or X-rays, from inflicted DNA damage, to cellular responses and biological consequences. Throughout this work, irradiation was performed with alpha-particles from 211A or X-rays. The induction and repair of double-strand breaks (DSBs) in human normal fibroblasts were investigated using pulsed-field gel electrophoresis and fragment analysis. The relative biological effectiveness (RBE) of 211At for DSB induction varied between 1.4 and 3.1. A small increase of DSBs was observed in cycling cells compared to stationary cells. The repair kinetics was slower after 211At and more residual damage was found after 24 h. Comparison between cells with different proliferation status showed that the repair was inefficient in cycling cells with more residual damage, regardless of radiation quality. Activation of cell cycle arrests was investigated using immunofluorescent labeling of the checkpoint kinase Chk2 and by measuring cell cycle distributions with flow cytometry analysis. After alpha-particle irradiation, the average number of Chk2-foci was larger and the cells had a more affected cell cycle progression for several weeks compared with X-irradiated cells, indicating a more powerful arrest after 211At

  2. Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

    Energy Technology Data Exchange (ETDEWEB)

    Yu Dindi; Ruangchaithaweesuk, Songtham; Yao Li; Xu Shoujun, E-mail: sxu7@uh.edu [University of Houston, Department of Chemistry (United States)

    2012-09-15

    The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/{radical}Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 {mu}m with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 {mu}m, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

  3. How antibodies alter the cell entry pathway of dengue virus particles in macrophages

    NARCIS (Netherlands)

    Ayala-Nunez, Nilda V.; Hoornweg, Tabitha E.; van de Pol, Denise P. I.; Sjollema, Klaas A.; Flipse, Jacky; van der Schaar, Hilde M.; Smit, Jolanda M.

    2016-01-01

    Antibody-dependent enhancement of dengue virus (DENV) infection plays an important role in the exacerbation of DENV-induced disease. To understand how antibodies influence the fate of DENV particles, we explored the cell entry pathway of DENV in the absence and presence of antibodies in macrophage-l

  4. Plume expansion of a laser-induced plasma studied with the particle-in-cell method

    DEFF Research Database (Denmark)

    Ellegaard, Ole; Nedela, T; Urbassek, H;

    2002-01-01

     The initial stage of laser-induced plasma plume expansion from a solid in vacuum and the effect of the Coulomb field have been studied. We have performed a one-dimensional numerical calculation by mapping the charge on a computational grid according to the particle-in-cell (PIC) method of Birdsall...

  5. Plume expansion of a laser-induced plasma studied with the particle-in-cell method

    DEFF Research Database (Denmark)

    Ellegaard, O.; Nedelea, T.; Schou, Jørgen;

    2002-01-01

    The initial stage of laser-induced plasma plume expansion from a solid in vacuum and the effect of the Coulomb field have been studied. We have performed a one-dimensional numerical calculation by mapping the charge on a computational grid according to the particle-in-cell (PIC) method of Birdsall...

  6. Viral particles drive rapid differentiation of memory B cells into secondary plasma cells producing increased levels of antibodies.

    Science.gov (United States)

    Zabel, Franziska; Mohanan, Deepa; Bessa, Juliana; Link, Alexander; Fettelschoss, Antonia; Saudan, Philippe; Kündig, Thomas M; Bachmann, Martin F

    2014-06-15

    Extensive studies have been undertaken to describe naive B cells differentiating into memory B cells at a cellular and molecular level. However, relatively little is known about the fate of memory B cells upon Ag re-encounter. We have previously established a system based on virus-like particles (VLPs), which allows tracking of VLP-specific B cells by flow cytometry as well as histology. Using allotype markers, it is possible to adoptively transfer memory B cells into a naive mouse and track responses of naive and memory B cells in the same mouse under physiological conditions. We have observed that VLP-specific memory B cells quickly differentiated into plasma cells that drove the early onset of a strong humoral IgG response. However, neither IgM(+) nor IgG(+) memory B cells proliferated extensively or entered germinal centers. Remarkably, plasma cells derived from memory B cells preferentially homed to the bone marrow earlier and secreted increased levels of Abs when compared with primary plasma cells derived from naive B cells. Hence, memory B cells have the unique phenotype to differentiate into highly effective secondary plasma cells.

  7. Preparation of nano-hydroxyapatite particles with different morphology and their response to highly malignant melanoma cells in vitro

    Science.gov (United States)

    Li, Bo; Guo, Bo; Fan, Hongsong; Zhang, Xingdong

    2008-11-01

    To investigate the effects of nano-hydroxyapatite (HA) particles with different morphology on highly malignant melanoma cells, three kinds of HA particles with different morphology were synthesized and co-cultured with highly malignant melanoma cells using phosphate-buffered saline (PBS) as control. A precipitation method with or without citric acid addition as surfactant was used to produce rod-like hydroxyapatite (HA) particles with nano- and micron size, respectively, and a novel oil-in-water emulsion method was employed to prepare ellipse-like nano-HA particles. Particle morphology and size distribution of the as prepared HA powders were characterized by transmission electron microscope (TEM) and dynamic light scattering technique. The nano- and micron HA particles with different morphology were co-cultured with highly malignant melanoma cells. Immunofluorescence analysis and MTT assay were employed to evaluate morphological change of nucleolus and proliferation of tumour cells, respectively. To compare the effects of HA particles on cell response, the PBS without HA particles was used as control. The experiment results indicated that particle nanoscale effect rather than particle morphology of HA was more effective for the inhibition on highly malignant melanoma cells proliferation.

  8. Preparation of nano-hydroxyapatite particles with different morphology and their response to highly malignant melanoma cells in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Li Bo [National Engineering Research Center for Biomaterial, Sichuan University, Chengdu 610064 (China); Guo Bo [National Engineering Research Center for Biomaterial, Sichuan University, Chengdu 610064 (China); West China Eye Center of Huaxi Hospital, Sichuan University, Chengdu 610064 (China); Fan Hongsong [National Engineering Research Center for Biomaterial, Sichuan University, Chengdu 610064 (China)], E-mail: leewave@126.com; Zhang Xingdong [National Engineering Research Center for Biomaterial, Sichuan University, Chengdu 610064 (China)

    2008-11-15

    To investigate the effects of nano-hydroxyapatite (HA) particles with different morphology on highly malignant melanoma cells, three kinds of HA particles with different morphology were synthesized and co-cultured with highly malignant melanoma cells using phosphate-buffered saline (PBS) as control. A precipitation method with or without citric acid addition as surfactant was used to produce rod-like hydroxyapatite (HA) particles with nano- and micron size, respectively, and a novel oil-in-water emulsion method was employed to prepare ellipse-like nano-HA particles. Particle morphology and size distribution of the as prepared HA powders were characterized by transmission electron microscope (TEM) and dynamic light scattering technique. The nano- and micron HA particles with different morphology were co-cultured with highly malignant melanoma cells. Immunofluorescence analysis and MTT assay were employed to evaluate morphological change of nucleolus and proliferation of tumour cells, respectively. To compare the effects of HA particles on cell response, the PBS without HA particles was used as control. The experiment results indicated that particle nanoscale effect rather than particle morphology of HA was more effective for the inhibition on highly malignant melanoma cells proliferation.

  9. Cell and tissue kinetics of the subependymal layer in mouse brain following heavy charged particle irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Manley, N.B.; Fabrikant, J.I.; Alpen, E.L.

    1988-12-01

    The following studies investigate the cellular response and cell population kinetics of the subependymal layer in the mouse brain exposed to heavy charged particle irradiation. Partial brain irradiation with helium and neon ions was confined to one cortex of the brain. Both the irradiated and the unirradiated contralateral cortex showed similar disturbances of the cell and tissue kinetics in the subependymal layers. The irradiated hemisphere exhibited histological damage, whereas the unirradiated side appeared normal histologically. This study concerns the cell population and cell cycle kinetics of the subependymal layer in the mouse brain, and the effects of charged particle irradiations on this cell population. Quantitative high resolution autoradiography was used to study the kinetic parameters in this cell layer. This study should help in understanding the effects of these high-energy heavy ions on normal mammalian brain tissue. The response of the mammalian brain exposure to charged particle ionizing radiation may be extremely variable. It varies from minimal physiological changes to overt tissue necrosis depending on a number of factors such as: the administered dose, dose-rate, the volume of the irradiated tissue, and the biological end-point being examined.

  10. Cells as Active Particles in Asymmetric Potentials: Motility under External Gradients

    Science.gov (United States)

    Comelles, Jordi; Caballero, David; Voituriez, Raphaël; Hortigüela, Verónica; Wollrab, Viktoria; Godeau, Amélie Luise; Samitier, Josep; Martínez, Elena; Riveline, Daniel

    2014-01-01

    Cell migration is a crucial event during development and in disease. Mechanical constraints and chemical gradients can contribute to the establishment of cell direction, but their respective roles remain poorly understood. Using a microfabricated topographical ratchet, we show that the nucleus dictates the direction of cell movement through mechanical guidance by its environment. We demonstrate that this direction can be tuned by combining the topographical ratchet with a biochemical gradient of fibronectin adhesion. We report competition and cooperation between the two external cues. We also quantitatively compare the measurements associated with the trajectory of a model that treats cells as fluctuating particles trapped in a periodic asymmetric potential. We show that the cell nucleus contributes to the strength of the trap, whereas cell protrusions guided by the adhesive gradients add a constant tunable bias to the direction of cell motion. PMID:25296303

  11. Silencing Bcl-2 Expression in Epithelial Cancer Cells Using “Smart” Particles

    Directory of Open Access Journals (Sweden)

    Yen-Ling Lin

    2014-09-01

    Full Text Available Short interfering RNA (siRNA targeted against anti-apoptotic Bcl-2 protein proved to knockdown its expression and trigger cancer cell death. We used degradable, pH-sensitive, comb-like [P(EAA-co-BMA-b-PNASI-g-P(HMA-co-TMAEMA] polymer to condense anti-Bcl-2 siRNA into “smart” particles, which proved to shuttle their cargo past the endosomal membrane and into the cytoplasm of HeLa and UM-SCC-17B cancer cells. HeLa and UM-SCC-17B cancer cells were treated with anti-Bcl-2 particles followed by quantifying Bcl-2 mRNA and protein levels using qRT-PCR and western blotting, respectively. “Smart” anti-Bcl-2 particles selectively suppress Bcl-2 mRNA and protein levels in HeLa cells by 50%–60% and 79%–81%, respectively. Similarly, “smart” anti-Bcl-2 particles inhibited Bcl-2 mRNA levels by 30%, 40%, and 20% upon incubation with UM-SCC-17B cancer cells for 48, 72, and 96 h, respectively. Bcl-2 protein expression in UM-SCC-17B cancer cells was inhibited by 30% after treatment for 72 h. Results show that pH-sensitive comb-like polymer complex anti-Bcl-2 siRNA forming “smart” nanoparticles that deliver their cargo into the cytoplasm of HeLa and UM-SCC-17B cancer cells causing Bcl-2 knockdown at the mRNA and protein levels.

  12. Continuous Electrokinetic Separation of Particles and Cells in a Serpentine Microchannel

    Science.gov (United States)

    Canter, Cameron; Zhu, Junjie; Tzeng, Tzuen Rong; Xuan, Xiangchun

    2010-11-01

    Particle separation plays an important role in many areas. A variety of force fields have been used to separate particles in microfluidic devices, among which electric field may be the most popular one due to its general applicability and adaptability. So far, however, electrophoresis-based separations have been limited to primarily batchwise processes. Dielectrophoresis (DEP)-based separations require in-channel micro-electrodes or micro-insulators to produce electric field gradients. In this talk we present a novel electrokinetic separation of particles in a serpentine microchannel. The continuous separation arises from the cross-stream particle dielectrophoresis induced by the non-uniform electric field inherent to curving microchannels. We demonstrate a size-based separation of polystyrene beads (1 μm and 5 μm in diameter) and microbial cells (E. coli and yeast) in the serpentine microchannel with the application of a small DC electric field. We also develop a numerical model to simulate the particle and cell separation processes.

  13. Influence of HDL particles on cell-cholesterol efflux under various pathological conditions.

    Science.gov (United States)

    Asztalos, Bela F; Horvath, Katalin V; Mehan, Michael; Yokota, Yuya; Schaefer, Ernst J

    2017-06-01

    It has been reported that low cell-cholesterol efflux capacity (CEC) of HDL is an independent risk factor for CVD. To better understand CEC regulation, we measured ABCA1- and scavenger receptor class B type I (SR-BI)-dependent cell-cholesterol efflux, HDL anti-oxidative capacity, HDL particles, lipids, and inflammatory- and oxidative-stress markers in 122 subjects with elevated plasma levels of triglyceride (TG), serum amyloid A (SAA), fibrinogen, myeloperoxidase (MPO), or β-sitosterol and in 146 controls. In controls, there were strong positive correlations between ABCA1-dependent cholesterol efflux and small preβ-1 concentrations (R(2) = 0.317) and SR-BI-dependent cholesterol efflux and large (α-1 + α-2) HDL particle concentrations (R(2) = 0.774). In high-TG patients, both the concentration and the functionality (preβ-1 concentration-normalized ABCA1 efflux) of preβ-1 particles were significantly elevated compared with controls; however, though the concentration of large particles was significantly decreased, their functionality (large HDL concentration-normalized SR-BI efflux) was significantly elevated. High levels of SAA or MPO were not associated with decreased functionality of either the small (preβ-1) or the large (α-1 + α-2) HDL particles. HDL anti-oxidative capacity was negatively influenced by high plasma β-sitosterol levels, but not by the concentrations of HDL particles, TG, SAA, fibrinogen, or MPO. Our data demonstrate that under certain conditions CEC is influenced not only by quantitative (concentration), but also by qualitative (functional) properties of HDL particles. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

  14. Wave-particle interactions with parallel whistler waves: Nonlinear and time-dependent effects revealed by particle-in-cell simulations

    Energy Technology Data Exchange (ETDEWEB)

    Camporeale, Enrico, E-mail: e.camporeale@cwi.nl [Center for Mathematics and Computer Science (CWI), 1098 XG Amsterdam (Netherlands); Zimbardo, Gaetano [Department of Physics, University of Calabria, Ponte P. Bucci, Cubo 31C, I-87036 Rende (Italy)

    2015-09-15

    We present a self-consistent Particle-in-Cell simulation of the resonant interactions between anisotropic energetic electrons and a population of whistler waves, with parameters relevant to the Earth's radiation belt. By tracking PIC particles and comparing with test-particle simulations, we emphasize the importance of including nonlinear effects and time evolution in the modeling of wave-particle interactions, which are excluded in the resonant limit of quasi-linear theory routinely used in radiation belt studies. In particular, we show that pitch angle diffusion is enhanced during the linear growth phase, and it rapidly saturates well before a single bounce period. This calls into question the widely used bounce average performed in most radiation belt diffusion calculations. Furthermore, we discuss how the saturation is related to the fact that the domain in which the particles pitch angle diffuses is bounded, and to the well-known problem of 90° diffusion barrier.

  15. Wave-particle interactions with parallel whistler waves: nonlinear and time-dependent effects revealed by Particle-in-Cell simulations

    CERN Document Server

    Camporeale, Enrico

    2014-01-01

    We present self-consistent Particle-in-Cell simulations of the resonant interactions between anisotropic energetic electrons and a population of whistler waves, with parameters relevant to the Earth's radiation belt. By tracking PIC particles, and comparing with test-particles simulations we emphasize the importance of including nonlinear effects and time evolution in the modeling of wave-particle interactions, which are excluded in the resonant limit of quasi-linear theory routinely used in radiation belt studies. In particular we show that pitch angle diffusion is enhanced during the linear growth phase, and it rapidly saturates. We discuss how the saturation is related to the fact that the domain in which the particles' pitch angle diffuse is bounded, and to the well-known problem of $90^\\circ$ diffusion barrier.

  16. Poly(2-oxazoline)-Based Microgel Particles for Neuronal Cell Culture.

    Science.gov (United States)

    Platen, Mitja; Mathieu, Evelien; Lück, Steffen; Schubel, René; Jordan, Rainer; Pautot, Sophie

    2015-05-11

    An increasing number of in vivo and in vitro neuro-engineering applications are making use of colloidal particles as neuronal cell carriers. Recent studies highlight the shortcomings of commercial glass particles and stress the benefit of using soft microgel particles (MGPs) instead. This study describes first the fabrication of MGPs from telechelic poly(2-methyl-2-oxazoline)s (PMeOx) cross-linkers and hydrophilic neutral (hydroxyethyl)methacrylate (HEMA) or charged 2-methacryloxyethyltrimethylammonium (METAC) monomers by emulsion polymerization, and it discusses their ability to support cell growth. It establishes that uncharged copolymers lead to MGPs with nonfouling properties inappropriate for cell culture, and it provides a protocol to amend their surface properties to enable cell adhesion. Finally, it demonstrates that the introduction of positive charges by METAC is necessary to obtain surface properties suitable for neuronal cell development. Through the optimization of the PMeOx30 MGP properties, this work provides general guidelines to evaluate and tune MGP chemistry to obtain microcarriers for neuro-engineering applications.

  17. Magnetic particle spectroscopy allows precise quantification of nanoparticles after passage through human brain microvascular endothelial cells

    Science.gov (United States)

    Gräfe, C.; Slabu, I.; Wiekhorst, F.; Bergemann, C.; von Eggeling, F.; Hochhaus, A.; Trahms, L.; Clement, J. H.

    2016-06-01

    Crossing the blood-brain barrier is an urgent requirement for the treatment of brain disorders. Superparamagnetic iron oxide nanoparticles (SPIONs) are a promising tool as carriers for therapeutics because of their physical properties, biocompatibility, and their biodegradability. In order to investigate the interaction of nanoparticles with endothelial cell layers in detail, in vitro systems are of great importance. Human brain microvascular endothelial cells are a well-suited blood-brain barrier model. Apart from generating optimal conditions for the barrier-forming cell units, the accurate detection and quantification of SPIONs is a major challenge. For that purpose we use magnetic particle spectroscopy to sensitively and directly quantify the SPION-specific iron content. We could show that SPION concentration depends on incubation time, nanoparticle concentration and location. This model system allows for further investigations on particle uptake and transport at cellular barriers with regard to parameters including particles’ shape, material, size, and coating.

  18. Cytotoxicity and genotoxicity induced by coal and coal fly ash particles samples in V79 cells.

    Science.gov (United States)

    León-Mejía, Grethel; Silva, Luis F O; Civeira, Matheus S; Oliveira, Marcos L S; Machado, Miriana; Villela, Izabel Vianna; Hartmann, Andreas; Premoli, Suziane; Corrêa, Dione Silva; Da Silva, Juliana; Henriques, João Antônio Pêgas

    2016-12-01

    Exposure to coal and coal ashes can cause harmful effects in in vitro and in vivo systems, mainly by the induction of oxidative damage. The aim of this work was to assess cytotoxic and genotoxic effects using the V79 cell line treated with coal and coal fly ash particles derived from a coal power plant located in Santa Catarina, Brazil. Two coal samples (COAL11 and COAL16) and two coal fly ash samples (CFA11 and CFA16) were included in this study. COAL16 was co-firing with a mixture of fuel oil and diesel oil. The comet assay data showed that exposure of V79 cells to coal and coal fly ash particles induced primary DNA lesions. Application of lesion-specific endonucleases (FPG and ENDO III) demonstrated increased DNA effects indicating the presence of high amounts of oxidative DNA lesions. The cytokinesis-block micronucleus cytome assay analysis showed that exposure of V79 cells to high concentrations of coal and coal fly ash particles induced cytotoxic effects (apoptosis and necrosis) and chromosomal instability (nucleoplasmic bridges, nuclear buds, and micronucleus (MN) formation). These results may be associated with compounds contained in the surface of the particles as hazardous elements, ultrafine/nanoparticles, and polycyclic aromatic hydrocarbons (PAHs) which were detected in the samples. Graphical abstract ᅟ.

  19. Geometric integration of the Vlasov-Maxwell system with a variational particle-in-cell scheme

    Science.gov (United States)

    Squire, Jonathan; Qin, Hong; Tang, William

    2012-10-01

    A fully variational, unstructured, electromagnetic particle-in-cell integrator is developed for integration of the Vlasov-Maxwell equations. Using the formalism of Discrete Exterior Calculus [1], the field solver, interpolation scheme and particle advance algorithm are derived through minimization of a single discrete field theory action. As a consequence of ensuring that the action is invariant under discrete electromagnetic gauge transformations, the integrator exactly conserves Gauss's law. This work was supported by USDOE Contract DE-AC02-09CH11466.[4pt] [1] M. Desbrun, A. N. Hirani, M. Leok, and J. E. Marsden, (2005), arXiv:math/0508341

  20. A Comparative Study of Electrolyte Flow and Slime Particle Transport in a Newly Designed Copper Electrolytic Cell and a Laboratory-Scale Conventional Electrolytic Cell

    Science.gov (United States)

    Zeng, Weizhi; Wang, Shijie; Free, Michael L.

    2016-08-01

    An innovative copper electrolytic cell was designed with its inlet at the cell top and its outlet near the cell bottom, in opposite to conventional electrolytic cells. It was modeled in COMSOL Multiphysics to simulate copper electrorefining process. Unlike conventional electrorefining cells, downward electrolyte flows are more dominant in the fluid flow field in this cell, which leads to faster settlement of slime particles and less contamination to the cathode. Copper concentration profiles, electrolyte flow velocity field, slime particle movements, and slime particle distributions were obtained as simulation results, which were compared with those in a laboratory-scale conventional electrolytic cell. Advantages of the newly designed electrolytic cell were found: copper ions are distributed more uniformly in the cell with a thinner diffusion layer near the cathode; stronger convection exists in the inter-electrode domain with dominant downward flows; and slime particles have larger possibilities to settle down and are less likely to reach the cathode.

  1. Numerical study on the complete blood cell sorting using particle tracing and dielectrophoresis in a microfluidic device

    Science.gov (United States)

    Ali, Haider; Park, Cheol Woo

    2016-11-01

    In this study, a numerical model of a microfluidic device with particle tracing and dielectrophoresis field-flow fractionation was employed to perform a complete and continuous blood cell sorting. A low voltage was applied to electrodes to separate the red blood cells, white blood cells, and platelets based on their cell size. Blood cell sorting and counting were performed by evaluating the cell trajectories, displacements, residence times, and recovery rates in the device. A novel numerical technique was used to count the number of separated blood cells by estimating the displacement and residence time of the cells in a microfluidic device. For successful blood cell sorting, the value of cells displacement must be approximately equal to or higher than the corresponding maximum streamwise distance. The study also proposed different outlet designs to improve blood cell separation. The basic outlet design resulted in a higher cells recovery rate than the other outlets design. The recovery rate decreased as the number of inlet cells and flow rates increased because of the high particle-particle interactions and collisions with walls. The particle-particle interactions significantly affect blood cell sorting and must therefore be considered in future work.

  2. Vector separation of particles and cells using an array of slanted open cavities

    CERN Document Server

    Bernate, Jorge A; Lagae, Liesbet; Konstantopoulo, Konstantinos; Drazer, German

    2014-01-01

    We present a microfluidic platform for the continuous separation of suspended particles based on their size and settling velocity. The separation method takes advantage of the flow field in the vicinity and inside a parallel array of slanted open cavities. These cavities induce flow along them, which deflects the suspended particles to a different degree depending on the extent to which they penetrate into the cavities. The cumulative deflection in the periodic array ultimately leads to vector chromatography, with the different species in the sample moving in different directions. We demonstrate density and size based separation over a range of flow rates by separating polystyrene and silica particles and show that purities nearing 100% can be achieved for multicomponent mixtures. We also demonstrate the potential of the platform to separate biological cells by fractionating different blood components. We discuss the presence of two regimes, which can be distinguished depending on the ratio between the settli...

  3. Apar-T: code, validation, and physical interpretation of particle-in-cell results

    CERN Document Server

    Melzani, Mickaël; Walder, Rolf; Folini, Doris; Favre, Jean M; Krastanov, Stefan; Messmer, Peter

    2013-01-01

    We present the parallel particle-in-cell (PIC) code Apar-T and, more importantly, address the fundamental question of the relations between the PIC model, the Vlasov-Maxwell theory, and real plasmas. First, we present four validation tests: spectra from simulations of thermal plasmas, linear growth rates of the relativistic tearing instability and of the filamentation instability, and non-linear filamentation merging phase. For the filamentation instability we show that the effective growth rates measured on the total energy can differ by more than 50% from the linear cold predictions and from the fastest modes of the simulation. Second, we detail a new method for initial loading of Maxwell-J\\"uttner particle distributions with relativistic bulk velocity and relativistic temperature, and explain why the traditional method with individual particle boosting fails. Third, we scrutinize the question of what description of physical plasmas is obtained by PIC models. These models rely on two building blocks: coarse...

  4. CPIC: A Parallel Particle-In-Cell Code for Studying Spacecraft Charging

    Science.gov (United States)

    Meierbachtol, Collin; Delzanno, Gian Luca; Moulton, David; Vernon, Louis

    2015-11-01

    CPIC is a three-dimensional electrostatic particle-in-cell code designed for use with curvilinear meshes. One of its primary objectives is to aid in studying spacecraft charging in the magnetosphere. CPIC maintains near-optimal computational performance and scaling thanks to a mapped logical mesh field solver, and a hybrid physical-logical space particle mover (avoiding the need to track particles). CPIC is written for parallel execution, utilizing a combination of both OpenMP threading and MPI distributed memory. New capabilities are being actively developed and added to CPIC, including the ability to handle multi-block curvilinear mesh structures. Verification results comparing CPIC to analytic test problems will be provided. Particular emphasis will be placed on the charging and shielding of a sphere-in-plasma system. Simulated charging results of representative spacecraft geometries will also be presented. Finally, its performance capabilities will be demonstrated through parallel scaling data.

  5. Finite grid instability and spectral fidelity of the electrostatic Particle-In-Cell algorithm

    Science.gov (United States)

    Huang, C.-K.; Zeng, Y.; Wang, Y.; Meyers, M. D.; Yi, S.; Albright, B. J.

    2016-10-01

    The origin of the Finite Grid Instability (FGI) is studied by resolving the dynamics in the 1D electrostatic Particle-In-Cell (PIC) model in the spectral domain at the single particle level and at the collective motion level. The spectral fidelity of the PIC model is contrasted with the underlying physical system or the gridless model. The systematic spectral phase and amplitude errors from the charge deposition and field interpolation are quantified for common particle shapes used in the PIC models. It is shown through such analysis and in simulations that the lack of spectral fidelity relative to the physical system due to the existence of aliased spatial modes is the major cause of the FGI in the PIC model.

  6. Effects of Alpha Particle and Proton Beam Irradiation as Putative Cross-Talk between A549 Cancer Cells and the Endothelial Cells in a Co-Culture System

    Energy Technology Data Exchange (ETDEWEB)

    Riquier, Hélène; Abel, Denis [URBC-NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000 (Belgium); Wera, Anne-Catherine; Heuskin, Anne-Catherine [LARN-PMR, NARILIS, University of Namur, Namur 5000 (Belgium); Genard, Géraldine [URBC-NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000 (Belgium); Lucas, Stéphane [LARN-PMR, NARILIS, University of Namur, Namur 5000 (Belgium); Michiels, Carine, E-mail: carine.michiels@unamur.be [URBC-NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000 (Belgium)

    2015-03-18

    Background: High-LET ion irradiation is being more and more often used to control tumors in patients. Given that tumors are now considered as complex organs composed of multiple cell types that can influence radiosensitivity, we investigated the effects of proton and alpha particle irradiation on the possible radioprotective cross-talk between cancer and endothelial cells. Materials and Methods: We designed new irradiation chambers that allow co-culture study of cells irradiated with a particle beam. A549 lung carcinoma cells and endothelial cells (EC) were exposed to 1.5 Gy of proton beam or 1 and 2 Gy of alpha particles. Cell responses were studied by clonogenic assays and cell cycle was analyzed by flow cytometry. Gene expression studies were performed using Taqman low density array and by RT-qPCR. Results: A549 cells and EC displayed similar survival fraction and they had similar cell cycle distribution when irradiated alone or in co-culture. Both types of irradiation induced the overexpression of genes involved in cell growth, inflammation and angiogenesis. Conclusions: We set up new irradiation chamber in which two cell types were irradiated together with a particle beam. We could not show that tumor cells and endothelial cells were able to protect each other from particle irradiation. Gene expression changes were observed after particle irradiation that could suggest a possible radioprotective inter-cellular communication between the two cell types but further investigations are needed to confirm these results.

  7. Effects of Alpha Particle and Proton Beam Irradiation as Putative Cross-Talk between A549 Cancer Cells and the Endothelial Cells in a Co-Culture System

    Directory of Open Access Journals (Sweden)

    Hélène Riquier

    2015-03-01

    Full Text Available Background: High-LET ion irradiation is being more and more often used to control tumors in patients. Given that tumors are now considered as complex organs composed of multiple cell types that can influence radiosensitivity, we investigated the effects of proton and alpha particle irradiation on the possible radioprotective cross-talk between cancer and endothelial cells. Materials and Methods: We designed new irradiation chambers that allow co-culture study of cells irradiated with a particle beam. A549 lung carcinoma cells and endothelial cells (EC were exposed to 1.5 Gy of proton beam or 1 and 2 Gy of alpha particles. Cell responses were studied by clonogenic assays and cell cycle was analyzed by flow cytometry. Gene expression studies were performed using Taqman low density array and by RT-qPCR. Results: A549 cells and EC displayed similar survival fraction and they had similar cell cycle distribution when irradiated alone or in co-culture. Both types of irradiation induced the overexpression of genes involved in cell growth, inflammation and angiogenesis. Conclusions: We set up new irradiation chamber in which two cell types were irradiated together with a particle beam. We could not show that tumor cells and endothelial cells were able to protect each other from particle irradiation. Gene expression changes were observed after particle irradiation that could suggest a possible radioprotective inter-cellular communication between the two cell types but further investigations are needed to confirm these results.

  8. Effects of Alpha Particle and Proton Beam Irradiation as Putative Cross-Talk between A549 Cancer Cells and the Endothelial Cells in a Co-Culture System

    Science.gov (United States)

    Riquier, Hélène; Abel, Denis; Wera, Anne-Catherine; Heuskin, Anne-Catherine; Genard, Géraldine; Lucas, Stéphane; Michiels, Carine

    2015-01-01

    Background: High-LET ion irradiation is being more and more often used to control tumors in patients. Given that tumors are now considered as complex organs composed of multiple cell types that can influence radiosensitivity, we investigated the effects of proton and alpha particle irradiation on the possible radioprotective cross-talk between cancer and endothelial cells. Materials and Methods: We designed new irradiation chambers that allow co-culture study of cells irradiated with a particle beam. A549 lung carcinoma cells and endothelial cells (EC) were exposed to 1.5 Gy of proton beam or 1 and 2 Gy of alpha particles. Cell responses were studied by clonogenic assays and cell cycle was analyzed by flow cytometry. Gene expression studies were performed using Taqman low density array and by RT-qPCR. Results: A549 cells and EC displayed similar survival fraction and they had similar cell cycle distribution when irradiated alone or in co-culture. Both types of irradiation induced the overexpression of genes involved in cell growth, inflammation and angiogenesis. Conclusions: We set up new irradiation chamber in which two cell types were irradiated together with a particle beam. We could not show that tumor cells and endothelial cells were able to protect each other from particle irradiation. Gene expression changes were observed after particle irradiation that could suggest a possible radioprotective inter-cellular communication between the two cell types but further investigations are needed to confirm these results. PMID:25794049

  9. Characterization of self-assembled virus-like particles of Merkel cell polyomavirus.

    Directory of Open Access Journals (Sweden)

    Tian-Cheng Li

    Full Text Available In our recombinant baculovirus system, VP1 protein of merkel cell polyomavirus (MCPyV, which is implicated as a causative agent in Merkel cell carcinoma, was self-assembled into MCPyV-like particles (MCPyV-LP with two different sizes in insect cells, followed by being released into the culture medium. DNA molecules of 1.5- to 5-kb, which were derived from host insect cells, were packaged in large, ~50-nm spherical particles but not in small, ~25-nm particles. Structure reconstruction using cryo-electron microscopy showed that large MCPyV-LPs are composed of 72 pentameric capsomeres arranged in a T = 7 icosahedral surface lattice and are 48 nm in diameter. The MCPyV-LPs did not share antigenic determinants with BK- and JC viruses (BKPyV and JCPyV. The VLP-based enzyme immunoassay was applied to investigate age-specific prevalence of MCPyV infection in the general Japanese population aged 1-70 years. While seroprevalence of MCPyV increased with age in children and young individuals, its seropositivity in each age group was lower compared with BKPyV and JCPyV.

  10. Charged particle mutagenesis at low dose and fluence in mouse splenic T cells

    Energy Technology Data Exchange (ETDEWEB)

    Grygoryev, Dmytro [Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239 (United States); Gauny, Stacey [Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Lasarev, Michael; Ohlrich, Anna [Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239 (United States); Kronenberg, Amy [Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Turker, Mitchell S., E-mail: turkerm@ohsu.edu [Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239 (United States); Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 (United States)

    2016-06-15

    Highlights: • Densely ionizing forms of space radiation induce mutations in splenic T cells at low fluence. • Large interstitial deletions and discontinuous LOH patterns are radiation signature mutations. • Space radiation mutagenesis suggests a cancer risk from deep space travel. - Abstract: High-energy heavy charged particles (HZE ions) found in the deep space environment can significantly affect human health by inducing mutations and related cancers. To better understand the relation between HZE ion exposure and somatic mutation, we examined cell survival fraction, Aprt mutant frequencies, and the types of mutations detected for mouse splenic T cells exposed in vivo to graded doses of densely ionizing {sup 48}Ti ions (1 GeV/amu, LET = 107 keV/μm), {sup 56}Fe ions (1 GeV/amu, LET = 151 keV/μm) ions, or sparsely ionizing protons (1 GeV, LET = 0.24 keV/μm). The lowest doses for {sup 48}Ti and {sup 56}Fe ions were equivalent to a fluence of approximately 1 or 2 particle traversals per nucleus. In most cases, Aprt mutant frequencies in the irradiated mice were not significantly increased relative to the controls for any of the particles or doses tested at the pre-determined harvest time (3–5 months after irradiation). Despite the lack of increased Aprt mutant frequencies in the irradiated splenocytes, a molecular analysis centered on chromosome 8 revealed the induction of radiation signature mutations (large interstitial deletions and complex mutational patterns), with the highest levels of induction at 2 particles nucleus for the {sup 48}Ti and {sup 56}Fe ions. In total, the results show that densely ionizing HZE ions can induce characteristic mutations in splenic T cells at low fluence, and that at least a subset of radiation-induced mutant cells are stably retained despite the apparent lack of increased mutant frequencies at the time of harvest.

  11. Zinc oxide particles induce inflammatory responses in vascular endothelial cells via NF-{kappa}B signaling

    Energy Technology Data Exchange (ETDEWEB)

    Tsou, Tsui-Chun, E-mail: tctsou@nhri.org.tw [Division of Environmental Health and Occupational Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan (China); Yeh, Szu-Ching; Tsai, Feng-Yuan; Lin, Ho-Jane [Division of Environmental Health and Occupational Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan (China); Cheng, Tsun-Jen [Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University, Taipei, Taiwan (China); Chao, How-Ran [Department of Environmental Science and Engineering, National Pingtung University of Science and Technology, Neipu, Pingtung, Taiwan (China); Tai, Lin-Ai [Center for Nanomedicine Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan (China)

    2010-11-15

    This study investigated inflammatory effects of zinc oxide (ZnO) particles on vascular endothelial cells. The effects of 50 and 100-nm ZnO particles on human umbilical vein endothelial cells (HUVECs) were characterized by assaying cytotoxicity, cell proliferation, and glutathione levels. A marked drop in survival rate was observed when ZnO concentration was increased to 45 {mu}g/ml. ZnO concentrations of {<=}3 {mu}g/ml resulted in increased cell proliferation, while those of {<=}45 {mu}g/ml caused dose-dependent increases in oxidized glutathione levels. Treatments with ZnO concentrations {<=}45 {mu}g/ml were performed to determine the expression of intercellular adhesion molecule-1 (ICAM-1) protein, an indicator of vascular endothelium inflammation, revealing that ZnO particles induced a dose-dependent increase in ICAM-1 expression and marked increases in NF-{kappa}B reporter activity. Overexpression of I{kappa}B{alpha} completely inhibited ZnO-induced ICAM-1 expression, suggesting NF-{kappa}B plays a pivotal role in regulation of ZnO-induced inflammation in HUVECs. Additionally, TNF-{alpha}, a typical inflammatory cytokine, induced ICAM-1 expression in an NF-{kappa}B-dependent manner, and ZnO synergistically enhanced TNF-{alpha}-induced ICAM-1 expression. Both 50 and 100-nm ZnO particles agglomerated to similar size distributions. This study reveals an important role for ZnO in modulating inflammatory responses of vascular endothelial cells via NF-{kappa}B signaling, which could have important implications for treatments of vascular disease.

  12. Nanostructural characterization of Sf9 cells during virus-like particles generation.

    Science.gov (United States)

    Lee, Gi-Ja; Lee, Su-Hwa; Lee, Young Ju; Quan, Fu-Shi

    2016-11-01

    Sf9 cells (a clonal isolate of Spodoptera frugiperda Sf21 cells) are commonly used to generate recombinant virus-like particles (VLPs). For VLPs generation, Sf9 cells are infected with recombinant baculoviruses (rBV) expressing desired proteins. During rBV infections, Sf9 cells have changes in cell diameters and surface structures. In this study, for the first time, we investigated nanostructural changes of Sf9 cells using atomic force microscopy (AFM) during VLPs generation containing Toxoplasma gondii rhoptry protein 18 (ROP 18). As results, Sf9 cells were changed to be larger at 2 days after rBV infections. They maintained their sizes and morphologies on day 3 and 4. Based on morphological (perimeter and diameter) and surface roughness (roughness average and root mean square) changes of Sf9 cells observed by AFM, we inferred that these nanostructural changes in Sf9 cell membranes might be due to the production and extrusion of VLPs after rBV infection. Our results suggest that shape and roughness parameters of Sf9 cell morphology and membrane surface by AFM could be very effective for quantitative analysis of VLP production. This study provides important information about structural and mechanochemical properties of Sf9 cells which are closely related with biological function. SCANNING 38:735-742, 2016. © 2016 Wiley Periodicals, Inc.

  13. A high-order WENO-Z finite difference based particle-source-in-cell method for computation of particle-laden flows with shocks

    Science.gov (United States)

    Jacobs, Gustaaf B.; Don, Wai-Sun

    2009-03-01

    A high-order particle-source-in-cell (PSIC) algorithm is presented for the computation of the interaction between shocks, small scale structures, and liquid and/or solid particles in high-speed engineering applications. The improved high-order finite difference weighted essentially non-oscillatory (WENO-Z) method for solution of the hyperbolic conservation laws that govern the shocked carrier gas flow, lies at the heart of the algorithm. Finite sized particles are modeled as points and are traced in the Lagrangian frame. The physical coupling of particles in the Lagrangian frame and the gas in the Eulerian frame through momentum and energy exchange, is numerically treated through high-order interpolation and weighing. The centered high-order interpolation of the fluid properties to the particle location is shown to lead to numerical instability in shocked flow. An essentially non-oscillatory interpolation (ENO) scheme is devised for the coupling that improves stability. The ENO based algorithm is shown to be numerically stable and to accurately capture shocks, small flow features and particle dispersion. Both the carrier gas and the particles are updated in time without splitting with a third-order Runge-Kutta TVD method. One and two-dimensional computations of a shock moving into a particle cloud demonstrates the characteristics of the WENO-Z based PSIC method (PSIC/WENO-Z). The PSIC/WENO-Z computations are not only in excellent agreement with the numerical simulations with a third-order Rusanov based PSIC and physical experiments in [V. Boiko, V.P. Kiselev, S.P. Kiselev, A. Papyrin, S. Poplavsky, V. Fomin, Shock wave interaction with a cloud of particles, Shock Waves, 7 (1997) 275-285], but also show a significant improvement in the resolution of small scale structures. In two-dimensional simulations of the Mach 3 shock moving into forty thousand bronze particles arranged in the shape of a rectangle, the long time accuracy of the high-order method is demonstrated

  14. Magnetic separation of particles and cells in ferrofluid flow through a straight microchannel using two offset magnets

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Jian; Deng, Yanxiang [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634-0921 (United States); Vedantam, Pallavi; Tzeng, Tzuen-Rong [Department of Biological Sciences, Clemson University, Clemson, SC 29634-0314 (United States); Xuan, Xiangchun, E-mail: xcxuan@clemson.edu [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634-0921 (United States)

    2013-11-15

    The separation of particles and cells is critical in many chemical and biological applications. This work presents a simple idea for utilizing a pair of permanent magnets to continuously separate diamagnetic particles and cells in ferrofluid flow through a straight microchannel. The first magnet is placed close to the microchannel for focusing the particle mixture to a single stream without the use of a sheath flow. The second magnet, which is offset from the first magnet and placed farther from the channel, is to displace the aligned particles to dissimilar flow paths for a continuous sorting. This idea is first demonstrated through the separation of 3 μm- and 10 μm-diameter polystyrene particles, where the effects of flow speed and magnet distance are both examined. The experimental data are found to fit well with the predictions of an analytical model. Furthermore, a continuous separation of live yeast cells from 10 μm polystyrene particles is implemented in the same device. - Highlights: • We develop a simple diamagnetic particle and cell separation technique in ferrofluids. • Two offset magnets are used to achieve a sheath-free continuous separation in a straight microchannel. • The technique is demonstrated through the magnetic separation of polystyrene particles and yeast cells. • The effects of ferrofluid speed and magnet-channel distance are examined on particle separation. • The predictions from an analytical model agree with the experimental data quantitatively.

  15. Understanding and exploiting nanoscale surface heterogeneity for particle and cell manipulation

    Science.gov (United States)

    Kalasin, Surachate

    signatures. Following the approach taken by biophysicists for describing the interactions of leukocytes with the endothelial vasculature near an injury, the state spaces in this thesis map regimes of free particle motion, immediate firm arrest, and persistent rolling against macroscopic average patch density, Debye length, particle size, and shear rate. Surprisingly, the electrostatic heterogeneity state space resembles that for selectin-mediated leukocyte motion, and reasons are put forth. This finding is important because it demonstrates how synthetic nanoscale constructs can be exploited to achieve the selective cell capture mechanism previously attributed only to specialized cell adhesion molecules. This thesis initiates studies that extend these fundamental principles, developed for a tunable and well-characterized synthetic model to biological systems. For instance, it is demonstrated that general behaviors seen with the electrostatic model are observed when fibrinogen proteins are substituted for the electrostatic patches. This shows that the nature of the attractions is immaterial to adhesion, and that the effect of added salt primarily alters the range of the electrostatic repulsion and, correspondingly, the contact area. Also, studies with Staphylococcus aureus run parallel to those employing 1 mum silica spheres, further translating the concepts. Inaugural studies with mammalian cells, in the future work section, indicate that application of the surface heterogeneity approach to cell manipulation holds much future promise.

  16. Acoustic separation of oil droplets, colloidal particles and their mixtures in a microfluidic cell

    KAUST Repository

    Vakarelski, Ivan Uriev

    2016-06-15

    Here we report direct macroscopic and microscopic observations of acoustic driven separation of dodecane oil droplets in water in the presence and absence of colloidal silica particles suspended in the water phase. The experiments were conducted in a simple rectangular channel glass microfluidic cell in which an ultrasound standing wave pattern was generated at 300 KHz frequency. The separation process of both oil droplets and colloidal particles inside the cell was recorded using a high-speed video camera equipped with a macro-objective lens for macroscopic observation or with a high-speed camera attached to an inverted optical microscope for a higher resolution microscopic observation. We characterize the clustering process in the case of emulsion droplets or solid colloidal particles and ultimately demonstrate the emulsion droplets separation from the solid particles in the mixtures based on their different acoustic contrast factors. Finally, we conduct proof of concept experiment to show that the same approach can be used in a continuous fluid flow process.

  17. Mesoscale Model for Blood Cell Adhesion and Transport using Ellipsoidal Particles

    Science.gov (United States)

    Chesnutt, Jennifer; Marshall, Jeffrey

    2008-11-01

    A novel discrete-element computational model for efficient transport, collision, and adhesion of ellipsoidal particles is applied to blood cells adhering through receptor-ligand binding in three-dimensional flow. The model has been used for simulation of over 13,000 adhesive cells through approximation of blood cells as elastic particles and other physically-justifiable approximations. The computational model is validated against experimental data of red blood cell (RBC) aggregation in shear and channel flows. The structure of aggregates formed by RBCs is analyzed by various measures that relate RBCs which are in contact with each other and that characterize an aggregate by fitting an ellipse to the projection of cells contained in the aggregate. Factors such as shear rate and adhesive surface energy density between cells are examined for their effects on the size and structure of RBC aggregates in both two- and three-dimensional computations. The effect of RBC aggregation on migration of blood elements (RBCs, leukocytes, platelets) in channel flow is also investigated.

  18. Effect of hydroxyapatite particle size, morphology and crystallinity on proliferation of colon cancer HCT116 cells

    Energy Technology Data Exchange (ETDEWEB)

    Dey, Sangeeta; Das, Mitun, E-mail: mitun@cgcri.res.in; Balla, Vamsi Krishna

    2014-06-01

    The aim of the present work is to chemically and physically characterize the synthesized Hydroxyapatite (HAp) micro and nanoparticles and to explore the inhibitory effect of nano-HAps on the in vitro growth of human colon cancerous cells HCT116. HAp powder was synthesized using three different routes to achieve micro and nanosized powders, with different morphologies and crystallinity. The synthesized powders were characterized using X-ray diffraction, FTIR spectroscopy and scanning electron microscope. The results showed that the average crystallite size of HAp powder varies from 11 nm to 177 nm and respective crystallinity of powder found to be in the range of 0.12 and 0.92. The effect of these physico-chemical properties of HAp powders on human colon cancer HCT116 cells inhibition was determined in vitro. It was found that decreasing the HAp powder crystallite size between 11 nm and 22 nm significantly increases the HCT116 cell inhibition. Our results demonstrate that apart from HAp powder size their crystallinity and morphology also play an important role in cellular inhibition of human colon cancer cells. - Highlights: • Chemically synthesized hydroxyapatite micro and nano-particles with different morphologies and crystallinity. • In vitro cell–material interaction showed that hydroxyapatite nano-particles inhibit colon cancer cells. • Human colon cancer cell inhibition also depends on crystallinity and morphology of HAp powder.

  19. Application of adaptive mesh refinement to particle-in-cell simulations of plasmas and beams

    Energy Technology Data Exchange (ETDEWEB)

    Vay, J.-L.; Colella, P.; Kwan, J.W.; McCorquodale, P.; Serafini, D.B.; Friedman, A.; Grote, D.P.; Westenskow, G.; Adam, J.-C.; Heron, A.; Haber, I.

    2003-11-04

    Plasma simulations are often rendered challenging by the disparity of scales in time and in space which must be resolved. When these disparities are in distinctive zones of the simulation domain, a method which has proven to be effective in other areas (e.g. fluid dynamics simulations) is the mesh refinement technique. We briefly discuss the challenges posed by coupling this technique with plasma Particle-In-Cell simulations, and present examples of application in Heavy Ion Fusion and related fields which illustrate the effectiveness of the approach. We also report on the status of a collaboration under way at Lawrence Berkeley National Laboratory between the Applied Numerical Algorithms Group (ANAG) and the Heavy Ion Fusion group to upgrade ANAG's mesh refinement library Chombo to include the tools needed by Particle-In-Cell simulation codes.

  20. Energy loss of intergalactic pair beams: Particle-in-Cell simulation

    CERN Document Server

    Kempf, Andreas; Spanier, Felix

    2016-01-01

    The change of the distribution function of electron-positron pair beams determines whether GeV photons can be produced as secondary radiation from TeV photons. We will discuss the instabilities driven by pair beams. The system of a thermal proton-electron plasma and the electron-positron beam is collision free. We have, therefore, used the Particle-in-Cell simulation approach. It was necessary to alter the physical parameters, but the ordering of growth rates has been retained. We were able to show that plasma instabilities can be recovered in particle-in-cell simulations, but their effect on the pair distribution function is negligible for beam-background energy density ratios typically found in blazars.

  1. Particle-in-cell simulations of plasma accelerators and electron-neutral collisions

    Energy Technology Data Exchange (ETDEWEB)

    Bruhwiler, David L.; Giacone, Rodolfo E.; Cary, John R.; Verboncoeur, John P.; Mardahl, Peter; Esarey, Eric; Leemans, W.P.; Shadwick, B.A.

    2001-10-01

    We present 2-D simulations of both beam-driven and laser-driven plasma wakefield accelerators, using the object-oriented particle-in-cell code XOOPIC, which is time explicit, fully electromagnetic, and capable of running on massively parallel supercomputers. Simulations of laser-driven wakefields with low ({approx}10{sup 16} W/cm{sup 2}) and high ({approx}10{sup 18} W/cm{sup 2}) peak intensity laser pulses are conducted in slab geometry, showing agreement with theory and fluid simulations. Simulations of the E-157 beam wakefield experiment at the Stanford Linear Accelerator Center, in which a 30 GeV electron beam passes through 1 m of preionized lithium plasma, are conducted in cylindrical geometry, obtaining good agreement with previous work. We briefly describe some of the more significant modifications of XOOPIC required by this work, and summarize the issues relevant to modeling relativistic electron-neutral collisions in a particle-in-cell code.

  2. A Particle In Cell code development for high current ion beam transport and plasma simulations

    CERN Document Server

    Joshi, N

    2016-01-01

    A simulation package employing a Particle in Cell (PIC) method is developed to study the high current beam transport and the dynamics of plasmas. This package includes subroutines those are suited for various planned projects at University of Frankfurt. In the framework of the storage ring project (F8SR) the code was written to describe the beam optics in toroidal magnetic fields. It is used to design an injection system for a ring with closed magnetic field lines. The generalized numerical model, in Cartesian coordinates is used to describe the intense ion beam transport through the chopper system in the low energy beam section of the FRANZ project. Especially for the chopper system, the Poisson equation is implemented with irregular geometries. The Particle In Cell model is further upgraded with a Monte Carlo Collision subroutine for simulation of plasma in the volume type ion source.

  3. Implementations of mesh refinement schemes for particle-in-cell plasma simulations

    Energy Technology Data Exchange (ETDEWEB)

    Vay, J.-L.; Colella, P.; Friedman, A.; Grote, D.P.; McCorquodale, P.; Serafini, D.B.

    2003-10-20

    Plasma simulations are often rendered challenging by the disparity of scales in time and in space which must be resolved. When these disparities are in distinctive zones of the simulation region, a method which has proven to be effective in other areas (e.g. fluid dynamics simulations) is the mesh refinement technique. We briefly discuss the challenges posed by coupling this technique with plasma Particle-In-Cell simulations and present two implementations in more detail, with examples.

  4. Development of Particle-in-Cell Simulation in a Two Dimensional Trench Geometry

    CERN Document Server

    Lin, Tai-Lu

    2016-01-01

    A two dimensional electrostatic Particle-in-Cell simulation code is developed to investigate anisotropy of ions in a trench geometry for plasma etching. The numerical simulation results suggest that if the trench width is larger than Debye length scale, anisotropy can be lost due to potential development across the trench. Furthermore, the effects of ion charge build up on the trench bottom is investigated, which can degrade the anisotropy.

  5. Thrust calculation of electric solar wind sail by particle-in-cell simulation

    OpenAIRE

    Hoshi, Kento; Kojima, Hirotsugu; Muranaka, Takanobu; YAMAKAWA, Hiroshi

    2016-01-01

    In this study, thrust characteristics of an electric solar wind sail were numerically evaluated using full three-dimensional particle-in-cell (PIC) simulation. The thrust obtained from the PIC simulation was lower than the thrust estimations obtained in previous studies. The PIC simulation indicated that ambient electrons strongly shield the electrostatic potential of the tether of the sail, and the strong shield effect causes a greater thrust reduction than has been obtaine...

  6. Columbia University microbeam: development of an experimentalsystem for targeting cells individually with counted particles

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Columbia University microbeam was constructed in 1993 andfinished by the end of 1995. It is well established and used routinely toirradiate cells in a highly localized spatial region with a defined number ofα-particles. By using this probe, it is possible to study a number ofradiobiological questions in ways that cannot be simulated by usingconventional broad-field exposures. This report describes the developmentand current capabilities of the Columbia University microbeam, as well as thepreliminary researches undertaken.

  7. First experience with particle-in-cell plasma physics code on ARM-based HPC systems

    Science.gov (United States)

    Sáez, Xavier; Soba, Alejandro; Sánchez, Edilberto; Mantsinen, Mervi; Mateo, Sergi; Cela, José M.; Castejón, Francisco

    2015-09-01

    In this work, we will explore the feasibility of porting a Particle-in-cell code (EUTERPE) to an ARM multi-core platform from the Mont-Blanc project. The used prototype is based on a system-on-chip Samsung Exynos 5 with an integrated GPU. It is the first prototype that could be used for High-Performance Computing (HPC), since it supports double precision and parallel programming languages.

  8. Particle-In-Cell/Monte Carlo Simulation of Ion Back Bombardment in Photoinjectors

    Energy Technology Data Exchange (ETDEWEB)

    Qiang, Ji; Corlett, John; Staples, John

    2009-03-02

    In this paper, we report on studies of ion back bombardment in high average current dc and rf photoinjectors using a particle-in-cell/Monte Carlo method. Using H{sub 2} ion as an example, we observed that the ion density and energy deposition on the photocathode in rf guns are order of magnitude lower than that in a dc gun. A higher rf frequency helps mitigate the ion back bombardment of the cathode in rf guns.

  9. NanOx, a new model to predict cell survival in the context of particle therapy

    Science.gov (United States)

    Cunha, M.; Monini, C.; Testa, E.; Beuve, M.

    2017-02-01

    Particle therapy is increasingly attractive for the treatment of tumors and the number of facilities offering it is rising worldwide. Due to the well-known enhanced effectiveness of ions, it is of utmost importance to plan treatments with great care to ensure tumor killing and healthy tissues sparing. Hence, the accurate quantification of the relative biological effectiveness (RBE) of ions, used in the calculation of the biological dose, is critical. Nevertheless, the RBE is a complex function of many parameters and its determination requires modeling. The approaches currently used have allowed particle therapy to thrive, but still show some shortcomings. We present herein a short description of a new theoretical framework, NanOx, to calculate cell survival in the context of particle therapy. It gathers principles from existing approaches, while addressing some of their weaknesses. NanOx is a multiscale model that takes the stochastic nature of radiation at nanometric and micrometric scales fully into account, integrating also the chemical aspects of radiation-matter interaction. The latter are included in the model by means of a chemical specific energy, determined from the production of reactive chemical species induced by irradiation. Such a production represents the accumulation of oxidative stress and sublethal damage in the cell, potentially generating non-local lethal events in NanOx. The complementary local lethal events occur in a very localized region and can, alone, lead to cell death. Both these classes of events contribute to cell death. The comparison between experimental data and model predictions for the V79 cell line show a good agreement. In particular, the dependence of the typical shoulders of cell survival curves on linear energy transfer are well described, but also the effectiveness of different ions, including the overkill effect. These results required the adjustment of a number of parameters compatible with the application of the model in

  10. Noise Removal with Maintained Spatial Resolution in Raman Images of Cells Exposed to Submicron Polystyrene Particles

    Directory of Open Access Journals (Sweden)

    Linnea Ahlinder

    2016-04-01

    Full Text Available The biodistribution of 300 nm polystyrene particles in A549 lung epithelial cells has been studied with confocal Raman spectroscopy. This is a label-free method in which particles and cells can be imaged without using dyes or fluorescent labels. The main drawback with Raman imaging is the comparatively low spatial resolution, which is aggravated in heterogeneous systems such as biological samples, which in addition often require long measurement times because of their weak Raman signal. Long measurement times may however induce laser-induced damage. In this study we use a super-resolution algorithm with Tikhonov regularization, intended to improve the image quality without demanding an increased number of collected pixels. Images of cells exposed to polystyrene particles have been acquired with two different step lengths, i.e., the distance between pixels, and compared to each other and to corresponding images treated with the super-resolution algorithm. It is shown that the resolution after application of super-resolution algorithms is not significantly improved compared to the theoretical limit for optical microscopy. However, to reduce noise and artefacts in the hyperspectral Raman images while maintaining the spatial resolution, we show that it is advantageous to use short mapping step lengths and super-resolution algorithms with appropriate regularization. The proposed methodology should be generally applicable for Raman imaging of biological samples and other photo-sensitive samples.

  11. Effect of particle size of Martian dust on the degradation of photovoltaic cell performance

    Science.gov (United States)

    Gaier, James R.; Perez-Davis, Marla E.

    1991-01-01

    Glass coverglass and SiO2 covered and uncovered silicon photovoltaic (PV) cells were subjected to conditions simulating a Mars dust storm, using the Martian Surface Wind Tunnel, to assess the effect of particle size on the performance of PV cells in the Martian environment. The dust used was an artificial mineral of the approximate elemental composition of Martian soil, which was sorted into four different size ranges. Samples were tested both initially clean and initially dusted. The samples were exposed to clear and dust laden winds, wind velocities varying from 23 to 116 m/s, and attack angles from 0 to 90 deg. It was found that transmittance through the coverglass approximates the power produced by a dusty PV cell. Occultation by the dust was found to dominate the performance degradation for wind velocities below 50 m/s, whereas abrasion dominates the degradation at wind velocities above 85 m/s. Occultation is most severe at 0 deg (parallel to the wind), is less pronounced from 22.5 to 67.5 deg, and is somewhat larger at 90 deg (perpendicular to the wind). Abrasion is negligible at 0 deg, and increases to a maximum at 90 deg. Occultation is more of a problem with small particles, whereas large particles (unless they are agglomerates) cause more abrasion.

  12. High speed versus pulsed images for micro-particle image velocimetry: a direct comparison of red blood cells versus fluorescing tracers as tracking particles.

    Science.gov (United States)

    Pitts, Katie L; Fenech, Marianne

    2013-10-01

    High speed photography in micro-particle image velocimetry (μPIV) using red blood cells as tracer particles and the use of fluorescing tracer particles (in conjunction with pulsed images) are directly compared by using both methods simultaneously. Measurements are taken on the same blood sample in the same microchip using both methods. This work directly and statistically compares the two methods of μPIV measurement in a controlled in vitro environment for the first time in literature. The pulsed method using fluorescing tracer particles is found to decrease the depth of correlation as expected, and to better represent the shape of the velocity profile. Two methods of velocity characterization are used (single and double parameter) and the pulsed images provide better shape representation in both cases.

  13. The role of particle-to-cell interactions in dictating nanoparticle aided magnetophoretic separation of microalgal cells

    Science.gov (United States)

    Toh, Pey Yi; Ng, Bee Wah; Ahmad, Abdul Latif; Chieh, Derek Chan Juinn; Lim, Jitkang

    2014-10-01

    Successful application of a magnetophoretic separation technique for harvesting biological cells often relies on the need to tag the cells with magnetic nanoparticles. This study investigates the underlying principle behind the attachment of iron oxide nanoparticles (IONPs) onto microalgal cells, Chlorella sp. and Nannochloropsis sp., in both freshwater and seawater, by taking into account the contributions of various colloidal forces involved. The complex interplay between van der Waals (vdW), electrostatic (ES) and Lewis acid-base interactions (AB) in dictating IONP attachment was studied under the framework of extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) analysis. Our results showed that ES interaction plays an important role in determining the net interaction between the Chlorella sp. cells and IONPs in freshwater, while the AB and vdW interactions play a more dominant role in dictating the net particle-to-cell interaction in high ionic strength media (>=100 mM NaCl), such as seawater. XDLVO predicted effective attachment between cells and surface functionalized IONPs (SF-IONPs) with an estimated secondary minimum of -3.12 kT in freshwater. This prediction is in accordance with the experimental observation in which 98.89% of cells can be magnetophoretically separated from freshwater with SF-IONPs. We have observed successful magnetophoretic separation of microalgal cells from freshwater and/or seawater for all the cases as long as XDLVO analysis predicts particle attachment. For both the conditions, no pH adjustment is required for particle-to-cell attachment.Successful application of a magnetophoretic separation technique for harvesting biological cells often relies on the need to tag the cells with magnetic nanoparticles. This study investigates the underlying principle behind the attachment of iron oxide nanoparticles (IONPs) onto microalgal cells, Chlorella sp. and Nannochloropsis sp., in both freshwater and seawater, by taking into account the

  14. Particle Swarm Optimization based predictive control of Proton Exchange Membrane Fuel Cell (PEMFC)

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Proton Exchange Membrane Fuel Cells (PEMFCs) are the main focus of their current development as power sources because they are capable of higher power density and faster start-up than other fuel cells. The humidification system and output performance of PEMFC stack are briefly analyzed. Predictive control of PEMFC based on Support Vector Regression Machine (SVRM) is presented and the SVRM is constructed. The processing plant is modelled on SVRM and the predictive control law is obtained by using Particle Swarm Optimization (PSO). The simulation and the results showed that the SVRM and the PSO receding optimization applied to the PEMFC predictive control yielded good performance.

  15. Particle Image Velocimetry and Computational Fluid Dynamics Analysis of Fuel Cell Manifold

    DEFF Research Database (Denmark)

    Lebæk, Jesper; Blazniak Andreasen, Marcin; Andresen, Henrik Assenholm

    2010-01-01

    The inlet effect on the manifold flow in a fuel cell stack was investigated by means of numerical methods (computational fluid dynamics) and experimental methods (particle image velocimetry). At a simulated high current density situation the flow field was mapped on a 70 cell simulated cathode...... manifold. Three different inlet configurations were tested: plug flow, circular inlet, and a diffuser inlet. A very distinct jet was formed in the manifold, when using the circular inlet configuration, which was confirmed both experimentally and numerically. This jet was found to be an asymmetric confined...

  16. HIV-1-Induced Small T Cell Syncytia Can Transfer Virus Particles to Target Cells through Transient Contacts

    Directory of Open Access Journals (Sweden)

    Menelaos Symeonides

    2015-12-01

    Full Text Available HIV-1 Env mediates fusion of viral and target cell membranes, but it can also mediate fusion of infected (producer and target cells, thus triggering the formation of multinucleated cells, so-called syncytia. Large, round, immobile syncytia are readily observable in cultures of HIV-1-infected T cells, but these fast growing “fusion sinks” are largely regarded as cell culture artifacts. In contrast, small HIV-1-induced syncytia were seen in the paracortex of peripheral lymph nodes and other secondary lymphoid tissue of HIV-1-positive individuals. Further, recent intravital imaging of lymph nodes in humanized mice early after their infection with HIV-1 demonstrated that a significant fraction of infected cells were highly mobile, small syncytia, suggesting that these entities contribute to virus dissemination. Here, we report that the formation of small, migratory syncytia, for which we provide further quantification in humanized mice, can be recapitulated in vitro if HIV-1-infected T cells are placed into 3D extracellular matrix (ECM hydrogels rather than being kept in traditional suspension culture systems. Intriguingly, live-cell imaging in hydrogels revealed that these syncytia, similar to individual infected cells, can transiently interact with uninfected cells, leading to rapid virus transfer without cell-cell fusion. Infected cells were also observed to deposit large amounts of viral particles into the extracellular space. Altogether, these observations suggest the need to further evaluate the biological significance of small, T cell-based syncytia and to consider the possibility that these entities do indeed contribute to virus spread and pathogenesis.

  17. PIV as a method for quantifying root cell growth and particle displacement in confocal images.

    Science.gov (United States)

    Bengough, A Glyn; Hans, Joachim; Bransby, M Fraser; Valentine, Tracy A

    2010-01-01

    Particle image velocimetry (PIV) quantifies displacement of patches of pixels between successive images. We evaluated PIV as a tool for microscopists by measuring displacements of cells and of a surrounding granular medium in confocal laser scanning microscopy images of Arabidopsis thaliana roots labeled with cell-membrane targeted green fluorescent protein. Excellent accuracy (e.g., displacement standard deviation PIV-predicted and actual displacements (r(2) > 0.83). Root mean squared error for these distorted images was 0.4-1.1 pixels, increasing at higher magnification factors. Cell growth and rhizosphere deformation were tracked with good temporal (e.g., 1-min interval) and spatial resolution, with PIV patches located on recognizable cell features being tracked more successfully. Appropriate choice of GFP-label was important to decrease small-scale biological noise due to intracellular motion. PIV of roots grown in stiff 2% versus 0.7% agar showed patterns of cell expansion consistent with physically impeded roots of other species. Roots in glass ballotini underwent rapid changes in growth direction on a timescale of minutes, associated with localized arching of ballotini. By tracking cell vertices, we monitored automatically cell length, width, and area every minute for 0.5 h for cells in different stages of development. In conclusion, PIV measured displacements successfully in images of living root cells and the external granular medium, revealing much potential for use by microscopists.

  18. Vaccination with dendritic cells pulsed with hepatitis C pseudo particles induces specific immune responses in mice

    Institute of Scientific and Technical Information of China (English)

    Kilian Weigand; Franziska Voigt; Jens Encke; Birgit Hoyler; Wolfgang Stremmel; Christoph Eisenbach

    2012-01-01

    AIM:To explore dendritic cells (DCs) multiple functions in immune modulation.METHODS:We used bone-marrow derived dendritic cells from BALB/c mice pulsed with pseudo particles from the hepatitis C virus to vaccinate naive BALB/c mice.Hepatitis C virus (HCV) pseudo particles consist of the genotype 1b derived envelope proteins E1 and E2,covering a non-HCV core structure.Thus,not a single epitope,but the whole "viral surface" induces immunogenicity.For vaccination,mature and activated DC were injected subcutaneously twice.RESULTS:Humoral and cellular immune responses measured by enzyme-linked immunosorbent assay and interferon-gamma enzyme-linked immunosorbent spot test showed antibody production as well as T-cells directed against HCV.Furthermore,T-cell responses confirmed two highly immunogenic regions in E1 and E2 outside the hypervariable region 1.CONCLUSION:Our results indicate dendritic cells as a promising vaccination model for HCV infection that should be evaluated further.

  19. Persistent oxidative stress in human neural stem cells exposed to low fluences of charged particles.

    Science.gov (United States)

    Baulch, Janet E; Craver, Brianna M; Tran, Katherine K; Yu, Liping; Chmielewski, Nicole; Allen, Barrett D; Limoli, Charles L

    2015-08-01

    Exposure to the space radiation environment poses risks for a range of deleterious health effects due to the unique types of radiation encountered. Galactic cosmic rays are comprised of a spectrum of highly energetic nuclei that deposit densely ionizing tracks of damage along the particle trajectory. These tracks are distinct from those generated by the more sparsely ionizing terrestrial radiations, and define the geometric distribution of the complex cellular damage that results when charged particles traverse the tissues of the body. The exquisite radiosensitivity of multipotent neural stem and progenitor cells found within the neurogenic regions of the brain predispose the central nervous system to elevated risks for radiation induced sequelae. Here we show that human neural stem cells (hNSC) exposed to different charged particles at space relevant fluences exhibit significant and persistent oxidative stress. Radiation induced oxidative stress was found to be most dependent on total dose rather than on the linear energy transfer of the incident particle. The use of redox sensitive fluorogenic dyes possessing relative specificity for hydroxyl radicals, peroxynitrite, nitric oxide (NO) and mitochondrial superoxide confirmed that most irradiation paradigms elevated reactive oxygen and nitrogen species (ROS and RNS, respectively) in hNSC over a 1 week interval following exposure. Nitric oxide synthase (NOS) was not the major source of elevated nitric oxides, as the use of NOS inhibitors had little effect on NO dependent fluorescence. Our data provide extensive evidence for the capability of low doses of charged particles to elicit marked changes in the metabolic profile of irradiated hNSC. Radiation induced changes in redox state may render the brain more susceptible to the development of neurocognitive deficits that could affect an astronaut's ability to perform complex tasks during extended missions in deep space. Copyright © 2015 The Authors. Published by

  20. Persistent oxidative stress in human neural stem cells exposed to low fluences of charged particles

    Directory of Open Access Journals (Sweden)

    Janet E. Baulch

    2015-08-01

    Full Text Available Exposure to the space radiation environment poses risks for a range of deleterious health effects due to the unique types of radiation encountered. Galactic cosmic rays are comprised of a spectrum of highly energetic nuclei that deposit densely ionizing tracks of damage along the particle trajectory. These tracks are distinct from those generated by the more sparsely ionizing terrestrial radiations, and define the geometric distribution of the complex cellular damage that results when charged particles traverse the tissues of the body. The exquisite radiosensitivity of multipotent neural stem and progenitor cells found within the neurogenic regions of the brain predispose the central nervous system to elevated risks for radiation induced sequelae. Here we show that human neural stem cells (hNSC exposed to different charged particles at space relevant fluences exhibit significant and persistent oxidative stress. Radiation induced oxidative stress was found to be most dependent on total dose rather than on the linear energy transfer of the incident particle. The use of redox sensitive fluorogenic dyes possessing relative specificity for hydroxyl radicals, peroxynitrite, nitric oxide (NO and mitochondrial superoxide confirmed that most irradiation paradigms elevated reactive oxygen and nitrogen species (ROS and RNS, respectively in hNSC over a 1 week interval following exposure. Nitric oxide synthase (NOS was not the major source of elevated nitric oxides, as the use of NOS inhibitors had little effect on NO dependent fluorescence. Our data provide extensive evidence for the capability of low doses of charged particles to elicit marked changes in the metabolic profile of irradiated hNSC. Radiation induced changes in redox state may render the brain more susceptible to the development of neurocognitive deficits that could affect an astronaut’s ability to perform complex tasks during extended missions in deep space.

  1. Modeling of electron-electron collisions for particle-in-cell simulations

    Energy Technology Data Exchange (ETDEWEB)

    Andrea, D. d' ; Munz, C.D.; Schneider, R.

    2006-09-15

    The modeling of the physics of pulsed plasma thrusters requires the numerical solution of the Boltzmann equation for rarefied plasma flows where continuum assumptions fail. To tackle this challenging task, a cooperation between several institutes has been formed with the goal to develop a hybrid code based on Particle-In-Cell and Direct Simulation Monte Carlo techniques. These development activities are bundled in the project ''Numerische Simulation und Auslegung eines instationaeren gepulsten magnetoplasmadynamischen Triebwerks fuer eine Mondsonde'' which is funded by the Landesstiftung Baden-Wuerttemberg within the subject area ''Modellierung und Simulation auf Hochleistungscomputern''. In the frame of this project, the IHM is in charge to develop suitable physical-mathematical and numerical models to include charged particle collisions into the simulation. which can significantly affect the Parameters of such plasma devices. The intention of the present report is to introduce the Fokker-Planck approach for electron-electron interaction in Standard charged particle simulations. where the impact Parameter is usually large resulting in a small deflection angle. The theoretical and applicative framework is discussed in detail paying particular attention to the Particle-In-Cell approach in velocity space. a new technique which allows the self-consistent computation of the friction and diffusion coefficients arising from the Fokker-Planck treatment of collisions. These velocity-dependent coefficients thernselves are responsible for the change in velocity of the simulation particles, which is determined by the numerical solution of a Langevin-type equation. Simulation results for typical numerical experiments computed with the new developed Fokker-Planck solver are presented. demonstrating the quality. property and reliability of the applied numerical methods. (orig.)

  2. THE CONVERGENCE OF PARTICLE-IN-CELL SCHEMES FOR COSMOLOGICAL DARK MATTER SIMULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Myers, Andrew; Colella, Phillip; Van Straalen, Brian, E-mail: ATMyers@lbl.gov [Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States)

    2016-01-10

    Particle methods are a ubiquitous tool for solving the Vlasov–Poisson equation in comoving coordinates, which is used to model the gravitational evolution of dark matter (DM) in an expanding universe. However, these methods are known to produce poor results on idealized test problems, particularly at late times, after the particle trajectories have crossed. To investigate this, we have performed a series of one- and two-dimensional “Zel’dovich pancake” calculations using the popular particle-in-cell (PIC) method. We find that PIC can indeed converge on these problems provided that the following modifications are made. The first modification is to regularize the singular initial distribution function by introducing a small but finite artificial velocity dispersion. This process is analogous to artificial viscosity in compressible gas dynamics, and, as with artificial viscosity, the amount of regularization can be tailored so that its effect outside of a well-defined region—in this case, the high-density caustics—is small. The second modification is the introduction of a particle remapping procedure that periodically reexpresses the DM distribution function using a new set of particles. We describe a remapping algorithm that is third-order accurate and adaptive in phase space. This procedure prevents the accumulation of numerical errors in integrating the particle trajectories from growing large enough to significantly degrade the solution. Once both of these changes are made, PIC converges at second order on the Zel’dovich pancake problem, even at late times, after many caustics have formed. Furthermore, the resulting scheme does not suffer from the unphysical, small-scale “clumping” phenomenon known to occur on the pancake problem when the perturbation wavevector is not aligned with one of the Cartesian coordinate axes.

  3. Intracellular viscoelasticity of HeLa cells during cell division studied by video particle-tracking microrheology.

    Science.gov (United States)

    Chen, Yin-Quan; Kuo, Chia-Yu; Wei, Ming-Tzo; Wu, Kelly; Su, Pin-Tzu; Huang, Chien-Shiou; Chiou, Arthur

    2014-01-01

    Cell division plays an important role in regulating cell proliferation and differentiation. It is managed by a complex sequence of cytoskeleton alteration that induces dividing cells to change their morphology to facilitate their division. The change in cytoskeleton structure is expected to affect the intracellular viscoelasticity, which may also contribute to cellular dynamic deformation during cell division. However, the intracellular viscoelasticity during cell division is not yet well understood. In this study, we injected 100-nm (diameter) carboxylated polystyrene beads into the cytoplasm of HeLa cells and applied video particle tracking microrheology to measure their intracellular viscoelasticity at different phases during cell division. The Brownian motion of the intracellular nanoprobes was analyzed to compute the viscoelasticity of HeLa cells in terms of the elastic modulus and viscous modulus as a function of frequency. Our experimental results indicate that during the course of cell division, both intracellular elasticity and viscosity increase in the transition from the metaphase to the anaphase, plausibly due to the remodeling of cytoskeleton and redistributions of molecular motors, but remain approximately the same from the anaphase to the telophase.

  4. Increasing the sensitivity for stem cell monitoring in system-function based magnetic particle imaging

    Science.gov (United States)

    Them, Kolja; Salamon, J.; Szwargulski, P.; Sequeira, S.; Kaul, M. G.; Lange, C.; Ittrich, H.; Knopp, Tobias

    2016-05-01

    The use of superparamagnetic iron oxide nanoparticles (SPIONs) has provided new possibilities in biophysics and biomedical imaging technologies. The magnetization dynamics of SPIONs, which can be influenced by the environment, are of central interest. In this work, different biological SPION environments are used to investigate three different calibration methods for stem cell monitoring in magnetic particle imaging. It is shown that calibrating using SPIONs immobilized via agarose gel or intracellular uptake results in superior stem cell image quality compared to mobile SPIONs in saline. This superior image quality enables more sensitive localization and identification of a significantly smaller number of magnetically labeled stem cells. The results are important for cell tracking and monitoring of future SPION based therapies such as hyperthermia based cancer therapies, targeted drug delivery, or tissue regeneration approaches where it is crucial to image a sufficiently small number of SPIONs interacting with biological matter.

  5. GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics

    CERN Document Server

    Blumers, Ansel L; Li, Zhen; Li, Xuejin; Karniadakis, George E

    2016-01-01

    Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 c...

  6. Critical Stokes number for the capture of inertial particles by recirculation cells in two-dimensional quasisteady flows

    Science.gov (United States)

    Verjus, Romuald; Angilella, Jean-Régis

    2016-05-01

    Inertial particles are often observed to be trapped, temporarily or permanently, by recirculation cells which are ubiquitous in natural or industrial flows. In the limit of small particle inertia, determining the conditions of trapping is a challenging task, as it requires a large number of numerical simulations or experiments to test various particle sizes or densities. Here, we investigate this phenomenon analytically and numerically in the case of heavy particles (e.g., aerosols) at low Reynolds number, to derive a trapping criterion that can be used both in analytical and numerical velocity fields. The resulting criterion allows one to predict the characteristics of trapped particles as soon as single-phase simulations of the flow are performed. Our analysis is valid for two-dimensional particle-laden flows in the vertical plane, in the limit where the particle inertia, the free-fall terminal velocity, and the flow unsteadiness can be treated as perturbations. The weak unsteadiness of the flow generally induces a chaotic tangle near heteroclinic or homoclinic cycles if any, leading to the apparent diffusion of fluid elements through the boundary of the cell. The critical particle Stokes number Stc below which aerosols also enter and exit the cell in a complex manner has been derived analytically, in terms of the flow characteristics. It involves the nondimensional curvature-weighted integral of the squared velocity of the steady fluid flow along the dividing streamline of the recirculation cell. When the flow is unsteady and St>Stc , a regular motion takes place due to gravity and centrifugal effects, like in the steady case. Particles driven towards the interior of the cell are trapped permanently. In contrast, when the flow is unsteady and Stparticles wander in a chaotic manner in the vicinity of the border of the cell, and can escape the cell.

  7. Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells

    NARCIS (Netherlands)

    van der Schaar, Hilde M.; Rust, Michael J.; Chen, Chen; van der Ende-Metselaar, Heidi; Wilschut, Jan; Zhuang, Xiaowei; Smit, Jolanda M.

    2008-01-01

    Dengue virus (DENV) is an enveloped RNA virus that causes the most common arthropod-borne infection worldwide. The mechanism by which DENV infects the host cell remains unclear. In this work, we used live-cell imaging and single-virus tracking to investigate the cell entry, endocytic trafficking, an

  8. Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells

    NARCIS (Netherlands)

    van der Schaar, Hilde M.; Rust, Michael J.; Chen, Chen; van der Ende-Metselaar, Heidi; Wilschut, Jan; Zhuang, Xiaowei; Smit, Jolanda M.

    2008-01-01

    Dengue virus (DENV) is an enveloped RNA virus that causes the most common arthropod-borne infection worldwide. The mechanism by which DENV infects the host cell remains unclear. In this work, we used live-cell imaging and single-virus tracking to investigate the cell entry, endocytic trafficking,

  9. Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells

    NARCIS (Netherlands)

    van der Schaar, Hilde M.; Rust, Michael J.; Chen, Chen; van der Ende-Metselaar, Heidi; Wilschut, Jan; Zhuang, Xiaowei; Smit, Jolanda M.

    2008-01-01

    Dengue virus (DENV) is an enveloped RNA virus that causes the most common arthropod-borne infection worldwide. The mechanism by which DENV infects the host cell remains unclear. In this work, we used live-cell imaging and single-virus tracking to investigate the cell entry, endocytic trafficking, an

  10. Fully implicit Particle-in-cell algorithms for multiscale plasma simulation

    Energy Technology Data Exchange (ETDEWEB)

    Chacon, Luis [Los Alamos National Laboratory

    2015-07-16

    The outline of the paper is as follows: Particle-in-cell (PIC) methods for fully ionized collisionless plasmas, explicit vs. implicit PIC, 1D ES implicit PIC (charge and energy conservation, moment-based acceleration), and generalization to Multi-D EM PIC: Vlasov-Darwin model (review and motivation for Darwin model, conservation properties (energy, charge, and canonical momenta), and numerical benchmarks). The author demonstrates a fully implicit, fully nonlinear, multidimensional PIC formulation that features exact local charge conservation (via a novel particle mover strategy), exact global energy conservation (no particle self-heating or self-cooling), adaptive particle orbit integrator to control errors in momentum conservation, and canonical momenta (EM-PIC only, reduced dimensionality). The approach is free of numerical instabilities: ωpeΔt >> 1, and Δx >> λD. It requires many fewer dofs (vs. explicit PIC) for comparable accuracy in challenging problems. Significant CPU gains (vs explicit PIC) have been demonstrated. The method has much potential for efficiency gains vs. explicit in long-time-scale applications. Moment-based acceleration is effective in minimizing NFE, leading to an optimal algorithm.

  11. Semiclassical modeling of quantum-mechanical multiparticle systems using parallel particle-in-cell methods

    Science.gov (United States)

    Dauger, Dean Edward

    2001-08-01

    We are successful in building a code that models many particle dynamic quantum systems by combining a semiclassical approximation of Feynman path integrals with parallel computing techniques (particle-in-cell) and numerical methods developed for simulating plasmas, establishing this approach as a viable technique for multiparticle time-dependent quantum mechanics. Run on high-performance parallel computers, this code applies semiclassical methods to simulate the time evolution of wavefunctions of many particles. We describe the analytical derivation and computational implementation of these techniques in detail. We present a study to thoroughly demonstrate the code's fidelity to quantum mechanics, resulting in innovative visualization and analysis techniques. We introduce and exhibit a method to address fermion particle statistics. We present studies of two quantum-mechanical problems: a two-electron, one- dimensional atom, resulting in high-quality extractions of one- and two-electron eigenstates, and electrostatic quasi-modes due to quantum effects in a hot electron plasma, relevant for predictions about stellar evolution. We supply discussions of alternative derivations, alternative implementations of the derivations, and an exploration of their consequences. Source code is shown throughout this dissertation. Finally, we present an extensive discussion of applications and extrapolations of this work, with suggestions for future direction.

  12. Parallelization of an implicit algorithm for multi-dimensional particle-in-cell simulations

    CERN Document Server

    Petrov, George M

    2013-01-01

    The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized using MPI (Message Passing Interface). Details on the algorithm implementation are given with emphasis on code optimization by overlapping computations with communications. Performance evaluation has been made on a small Linux cluster with 32 processors for two typical regimes of PIC operation: "particle dominated", for which the bulk of the computation time is spent on pushing particles, and "field dominated", for which computing the fields is prevalent. We found that the MPI implementation of the code offers a significant numerical speedup. In the "particle dominated" regime it is close to the maximum theoretical one, while in the other regime it is about 75-80 % of the maximum speed-up. The code parallelization will allow future implementation of atomic physics and exte...

  13. Effect of particle clustering of silver nanoparticles on ultrathin silicon solar cell

    Science.gov (United States)

    Shokeen, Poonam; Jain, Amit; Kapoor, Avinashi; Gupta, Vinay

    2016-07-01

    Particle clustering is a major concern for uniform dispersal of nanoparticles in various deposition procedures. Well separated uniform distribution of metal nanoparticles is essential for effective coupling of surface plasmons. This work experimentally and theoretically, discusses the effect of nanoparticle clustering on the light trapping efficiency of silver nanoparticles. Pulsed laser deposition system has been used for deposition of silver nanoparticles, and substrate heating has been used to promote uniform distribution of nanoparticles. Pre-heated substrate depositions are compared with corresponding post-annealed samples. XRD, FESEM, Photoluminescence and UV-visible spectroscopy have been used to study the variations in their structural and optical properties. Mono-dispersal of silver nanoparticles for pre-heated substrates results in sharper surface plasmon resonance in comparison to post-annealed samples. Mie theory is used to estimate the particle size of the nanoparticles and findings are in accordance with quantitative analysis of FESEM images. Finite-difference time domain technique is used to discuss the effect of particle distribution on an ultrathin film silicon solar cell. Device degradation is observed as a result of clustering of silver nanoparticles. Hence, mono-dispersal of plasmonic nanostructures is important for required results and pre-heated deposition of metal nanoparticles by pulsed laser deposition can effectively solve the problem of particle clustering.

  14. Darkfield-Confocal Microscopy detection of nanoscale particle internalization by human lung cells

    Directory of Open Access Journals (Sweden)

    Samet James M

    2011-01-01

    Full Text Available Abstract Background Concerns over the health effects of nanomaterials in the environment have created a need for microscopy methods capable of examining the biological interactions of nanoparticles (NP. Unfortunately, NP are beyond the diffraction limit of resolution for conventional light microscopy (~200 nm. Fluorescence and electron microscopy techniques commonly used to examine NP interactions with biological substrates have drawbacks that limit their usefulness in toxicological investigation of NP. EM is labor intensive and slow, while fluorescence carries the risk of photobleaching the sample and has size resolution limits. In addition, many relevant particles lack intrinsic fluorescence and therefore can not be detected in this manner. To surmount these limitations, we evaluated the potential of a novel combination of darkfield and confocal laser scanning microscopy (DF-CLSM for the efficient 3D detection of NP in human lung cells. The DF-CLSM approach utilizes the contrast enhancements of darkfield microscopy to detect objects below the diffraction limit of 200 nm based on their light scattering properties and interfaces it with the power of confocal microscopy to resolve objects in the z-plane. Results Validation of the DF-CLSM method using fluorescent polystyrene beads demonstrated spatial colocalization of particle fluorescence (Confocal and scattered transmitted light (Darkfield along the X, Y, and Z axes. DF-CLSM imaging was able to detect and provide reasonable spatial locations of 27 nm TiO2 particles in relation to the stained nuclei of exposed BEAS 2B cells. Statistical analysis of particle proximity to cellular nuclei determined a significant difference between 5 min and 2 hr particle exposures suggesting a time-dependant internalization process. Conclusions DF-CLSM microscopy is an alternative to current conventional light and electron microscopy methods that does not rely on particle fluorescence or contrast in electron

  15. Understanding the mechanisms of sickle cell disease by simulations with a discrete particle model

    Science.gov (United States)

    Hui, Katrina; Lin, Guang; Pan, Wenxiao

    2013-01-01

    Sickle cell disease (SCD) is an inherited blood disorder characterized by rigid, sickle-shaped red blood cells (RBCs). Because of their rigidity and shape, sickle cells can get stuck in smaller blood vessels, causing blockages and depriving oxygen to tissues. This study develops and applies mathematical models to better understand the mechanism of SCD. Two-dimensional models of RBCs and blood vessels have been constructed by representing them as discrete particles interacting with different forces. The nonlinear, elastic property of healthy RBCs could be adequately reproduced using a cosine angle bending force and a worm-like chain spring force. With the ability to deform, RBCs can squeeze through narrow blood vessels. In modeling sickle cells as rigid bodies and applying repelling and friction forces from the blood vessel, this study shows that geometrical factors (dimensions of the sickle cell and blood vessels) as well as rigidity and adhesiveness of the sickle cell all play an important role in determining how, and if, sickle cells become trapped within narrow blood capillaries. With lack of data to validate the model, this study primarily provides a sensitivity analysis of factors influencing sickle cell occlusion and identified critical data to support future modeling.

  16. Increasing magnetite contents of polymeric magnetic particles dramatically improves labeling of neural stem cell transplant populations.

    Science.gov (United States)

    Adams, Christopher F; Rai, Ahmad; Sneddon, Gregor; Yiu, Humphrey H P; Polyak, Boris; Chari, Divya M

    2015-01-01

    Safe and efficient delivery of therapeutic cells to sites of injury/disease in the central nervous system is a key goal for the translation of clinical cell transplantation therapies. Recently, 'magnetic cell localization strategies' have emerged as a promising and safe approach for targeted delivery of magnetic particle (MP) labeled stem cells to pathology sites. For neuroregenerative applications, this approach is limited by the lack of available neurocompatible MPs, and low cell labeling achieved in neural stem/precursor populations. We demonstrate that high magnetite content, self-sedimenting polymeric MPs [unfunctionalized poly(lactic acid) coated, without a transfecting component] achieve efficient labeling (≥90%) of primary neural stem cells (NSCs)-a 'hard-to-label' transplant population of major clinical relevance. Our protocols showed high safety with respect to key stem cell regenerative parameters. Critically, labeled cells were effectively localized in an in vitro flow system by magnetic force highlighting the translational potential of the methods used. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Targeted drug delivery to circulating tumor cells via platelet membrane-functionalized particles.

    Science.gov (United States)

    Li, Jiahe; Ai, Yiwei; Wang, Lihua; Bu, Pengcheng; Sharkey, Charles C; Wu, Qianhui; Wun, Brittany; Roy, Sweta; Shen, Xiling; King, Michael R

    2016-01-01

    Circulating tumor cells (CTCs) are responsible for metastases in distant organs via hematogenous dissemination. Fundamental studies in the past decade have suggested that neutralization of CTCs in circulation could represent an effective strategy to prevent metastasis. Current paradigms of targeted drug delivery into a solid tumor largely fall into two main categories: unique cancer markers (e.g. overexpression of surface receptors) and tumor-specific microenvironment (e.g. low pH, hypoxia, etc.). While relying on a surface receptor to target CTCs can be greatly challenged by cancer heterogeneity, targeting of tumor microenvironments has the advantage of recognizing a broader spectrum of cancer cells regardless of genetic differences or tumor types. The blood circulation, however, where CTCs transit through, lacks the same tumor microenvironment as that found in a solid tumor. In this study, a unique "microenvironment" was confirmed upon introduction of cancer cells of different types into circulation where activated platelets and fibrin were physically associated with blood-borne cancer cells. Inspired by this observation, synthetic silica particles were functionalized with activated platelet membrane along with surface conjugation of tumor-specific apoptosis-inducing ligand cytokine, TRAIL. Biomimetic synthetic particles incorporated into CTC-associated micro-thrombi in lung vasculature and dramatically decreased lung metastases in a mouse breast cancer metastasis model. Our results demonstrate a "Trojan Horse" strategy of neutralizing CTCs to attenuate metastasis.

  18. Three-dimensional single-particle tracking in live cells: news from the third dimension

    Science.gov (United States)

    Dupont, A.; Gorelashvili, M.; Schüller, V.; Wehnekamp, F.; Arcizet, D.; Katayama, Y.; Lamb, D. C.; Heinrich, D.

    2013-07-01

    Single-particle tracking (SPT) is of growing importance in the biophysical community. It is used to investigate processes such as drug and gene delivery, viral uptake, intracellular trafficking or membrane-bound protein mobility. Traditionally, SPT is performed in two dimensions (2D) because of its technical simplicity. However, life occurs in three dimensions (3D) and many methods have been recently developed to track particles in 3D. Now, is the third dimension worth the effort? Here we investigate the differences between the 2D and 3D analyses of intracellular transport with the 3D development of a time-resolved mean square displacement (MSD) analysis introduced previously. The 3D trajectories, and the 2D projections, of fluorescent nanoparticles were obtained with an orbital tracking microscope in two different cell types: in Dictyostelium discoideum ameba and in adherent, more flattened HuH-7 human cells. As expected from the different 3D organization of both cells’ cytoskeletons, a third of the active transport was lost upon projection in the ameba whereas the identification of the active phases was barely affected in the HuH-7 cells. In both cell types, we found intracellular diffusion to be anisotropic and the diffusion coefficient values derived from the 2D analysis were therefore biased.

  19. Particle Size-Dependent Antibacterial Activity and Murine Cell Cytotoxicity Induced by Graphene Oxide Nanomaterials

    Directory of Open Access Journals (Sweden)

    Lin Zhao

    2016-01-01

    Full Text Available Recent studies have indicated that graphene and its derivative graphene oxide (GO engage in a wide range of antibacterial activities with limited toxicity to human cells. Here, we systematically evaluate the dependence of GO toxicity on the size of the nanoparticles used in treatments: we compare the cytotoxic effects of graphene quantum dots (GQDs, <15 nm, small GOs (SGOs, 50–200 nm, and large GOs (LGOs, 0.5–3 μm. We synthesize the results of bacterial colony count assays and SEM-based observations of morphological changes to assess the antibacterial properties that these GOs bring into effect against E. coli. We also use Live/Dead assays and morphological analysis to investigate changes to mammalian (Murine macrophage-like Raw 264.7 cells induced by the presence of the various GO particle types. Our results demonstrate that LGOs, SGOs, and GQDs possess antibacterial activities and cause mammalian cell cytotoxicity at descending levels of potency. Placing our observations in the context of previous simulation results, we suggest that both the lateral size and surface area of GO particles contribute to cytotoxic effects. We hope that the size dependence elucidated here provides a useful schematic for tuning GO-cell interactions in biomedical applications.

  20. Targeted drug delivery to circulating tumor cells via platelet membrane-functionalized particles

    Science.gov (United States)

    Li, Jiahe; Ai, Yiwei; Wang, Lihua; Bu, Pengcheng; Sharkey, Charles C.; Wu, Qianhui; Wun, Brittany; Roy, Sweta; Shen, Xiling; King, Michael R.

    2015-01-01

    Circulating tumor cells (CTCs) are responsible for metastases in distant organs via hematogenous dissemination. Fundamental studies in the past decade have suggested that neutralization of CTCs in circulation could represent an effective strategy to prevent metastasis. Current paradigms of targeted drug delivery into a solid tumor largely fall into two main categories: unique cancer markers (e.g. overexpression of surface receptors) and tumor-specific microenvironment (e.g. low pH, hypoxia, etc.). While relying on a surface receptor to target CTCs can be greatly challenged by cancer heterogeneity, targeting of tumor microenvironments has the advantage of recognizing a broader spectrum of cancer cells regardless of genetic differences or tumor types. The blood circulation, however, where CTCs transit through, lacks the same tumor microenvironment as that found in a solid tumor. In this study, a unique “microenvironment” was confirmed upon introduction of cancer cells of different types into circulation where activated platelets and fibrin were physically associated with blood-borne cancer cells. Inspired by this observation, synthetic silica particles were functionalized with activated platelet membrane along with surface conjugation of tumor-specific apoptosis-inducing ligand cytokine, TRAIL. Biomimetic synthetic particles incorporated into CTC-associated micro-thrombi in lung vasculature and dramatically decreased lung metastases in a mouse breast cancer metastasis model. Our results demonstrate a “Trojan Horse” strategy of neutralizing CTCs to attenuate metastasis. PMID:26519648

  1. Particle-In-Cell Simulation of Electron Acceleration in Solar Coronal Jets

    CERN Document Server

    Baumann, G

    2012-01-01

    We investigate electron acceleration resulting from 3D magnetic reconnection between an emerging, twisted magnetic flux rope and a pre-existing weak, open magnetic field. We first follow the rise of an unstable, twisted flux tube with a resistive MHD simulation where the numerical resolution is enhanced by using fixed mesh refinement. As in previous MHD investigations of similar situations the rise of the flux tube into the pre-existing inclined coronal magnetic field results in the formation of a solar coronal jet. A snapshot of the MHD model is then used as an initial and boundary condition for a particle-in-cell simulation, using up to half a billion cells and over 20 billion charged particle. Particle acceleration occurs mainly in the reconnection current sheet, with accelerated electrons displaying a power law dN/dE distribution with an index of about -1.65. The main acceleration mechanism is a systematic electric field, striving to maintaining the electric current in the current sheet against losses cau...

  2. Particle-in-cell Simulation of Electron Acceleration in Solar Coronal Jets

    Science.gov (United States)

    Baumann, G.; Nordlund, Å.

    2012-11-01

    We investigate electron acceleration resulting from three-dimensional magnetic reconnection between an emerging, twisted magnetic flux rope and a pre-existing weak, open magnetic field. We first follow the rise of an unstable, twisted flux tube with a resistive MHD simulation where the numerical resolution is enhanced by using fixed mesh refinement. As in previous MHD investigations of similar situations, the rise of the flux tube into the pre-existing inclined coronal magnetic field results in the formation of a solar coronal jet. A snapshot of the MHD model is then used as an initial and boundary condition for a particle-in-cell simulation, using up to half a billion cells and over 20 billion charged particles. Particle acceleration occurs mainly in the reconnection current sheet, with accelerated electrons displaying a power law in the energy probability distribution with an index of around -1.5. The main acceleration mechanism is a systematic electric field, striving to maintaining the electric current in the current sheet against losses caused by electrons not being able to stay in the current sheet for more than a few seconds at a time.

  3. Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells In Vivo.

    Science.gov (United States)

    Zheng, Bo; von See, Marc P; Yu, Elaine; Gunel, Beliz; Lu, Kuan; Vazin, Tandis; Schaffer, David V; Goodwill, Patrick W; Conolly, Steven M

    2016-01-01

    Stem cell therapies have enormous potential for treating many debilitating diseases, including heart failure, stroke and traumatic brain injury. For maximal efficacy, these therapies require targeted cell delivery to specific tissues followed by successful cell engraftment. However, targeted delivery remains an open challenge. As one example, it is common for intravenous deliveries of mesenchymal stem cells (MSCs) to become entrapped in lung microvasculature instead of the target tissue. Hence, a robust, quantitative imaging method would be essential for developing efficacious cell therapies. Here we show that Magnetic Particle Imaging (MPI), a novel technique that directly images iron-oxide nanoparticle-tagged cells, can longitudinally monitor and quantify MSC administration in vivo. MPI offers near-ideal image contrast, depth penetration, and robustness; these properties make MPI both ultra-sensitive and linearly quantitative. Here, we imaged, for the first time, the dynamic trafficking of intravenous MSC administrations using MPI. Our results indicate that labeled MSC injections are immediately entrapped in lung tissue and then clear to the liver within one day, whereas standard iron oxide particle (Resovist) injections are immediately taken up by liver and spleen. Longitudinal MPI-CT imaging also indicated a clearance half-life of MSC iron oxide labels in the liver at 4.6 days. Finally, our ex vivo MPI biodistribution measurements of iron in liver, spleen, heart, and lungs after injection showed excellent agreement (R(2) = 0.943) with measurements from induction coupled plasma spectrometry. These results demonstrate that MPI offers strong utility for noninvasively imaging and quantifying the systemic distribution of cell therapies and other therapeutic agents.

  4. On the effect of particle size distribution on the discharge performance of nickel-metal hydride cells

    Energy Technology Data Exchange (ETDEWEB)

    Heikonen, J.M. [Center for Scientific Computing, Espoo (Finland); Nagarajan, G.S.; Zee, J.W. van [Department of Chemical Engineering, University of South Carolina, Columbia, SC (United States)

    1997-12-31

    The effect of particle size distribution on the discharge performance of nickel-metal hydride cells with mathematical models is investigated. A model with a continuous size distribution is presented and a simplified discrete version with two particle sizes is numerically analyzed for various parameter values. Simulation results are compared with experiments from another article and the deviations are analyzed. (orig.) 13 refs.

  5. Differential roles of the protein corona in the cellular uptake of nanoporous polymer particles by monocyte and macrophage cell lines.

    Science.gov (United States)

    Yan, Yan; Gause, Katelyn T; Kamphuis, Marloes M J; Ang, Ching-Seng; O'Brien-Simpson, Neil M; Lenzo, Jason C; Reynolds, Eric C; Nice, Edouard C; Caruso, Frank

    2013-12-23

    Many biomolecules, mainly proteins, adsorb onto polymer particles to form a dynamic protein corona in biological environments. The protein corona can significantly influence particle-cell interactions, including internalization and pathway activation. In this work, we demonstrate the differential roles of a given protein corona formed in cell culture media in particle uptake by monocytes and macrophages. By exposing disulfide-stabilized poly(methacrylic acid) nanoporous polymer particles (PMASH NPPs) to complete cell growth media containing 10% fetal bovine serum, a protein corona, with the most abundant component being bovine serum albumin, was characterized. Upon adsorption onto the PMASH NPPs, native bovine serum albumin (BSA) was found to undergo conformational changes. The denatured BSA led to a significant decrease in internalization efficiency in human monocytic cells, THP-1, compared with the bare particles, due to reduced cell membrane adhesion. In contrast, the unfolded BSA on the NPPs triggered class A scavenger receptor-mediated phagocytosis in differentiated macrophage-like cells (dTHP-1) without a significant impact on the overall internalization efficiency. Taken together, this work demonstrates the disparate effects of a given protein corona on particle-cell interactions, highlighting the correlation between protein corona conformation in situ and relevant biological characteristics for biological functionalities.

  6. Fluid preconditioning for Newton-Krylov-based, fully implicit, electrostatic particle-in-cell simulations

    CERN Document Server

    Chen, Guangye; Leibs, Christopher A; Knoll, Dana A; Taitano, William

    2013-01-01

    A recent proof-of-principle study proposes an energy- and charge-conserving, nonlinearly implicit electrostatic particle-in-cell (PIC) algorithm in one dimension [Chen et al, J. Comput. Phys., 230 (2011) 7018]. The algorithm in the reference employs an unpreconditioned Jacobian-free Newton-Krylov method, which ensures nonlinear convergence at every timestep (resolving the dynamical timescale of interest). Kinetic enslavement, which is one key component of the algorithm, not only enables fully implicit PIC a practical approach, but also allows preconditioning the kinetic solver with a fluid approximation. This study proposes such a preconditioner, in which the linearized moment equations are closed with moments computed from particles. Effective acceleration of the linear GMRES solve is demonstrated, on both uniform and non-uniform meshes. The algorithm performance is largely insensitive to the electron-ion mass ratio. Numerical experiments are performed on a 1D multi-scale ion acoustic wave test problem.

  7. On the Numerical Dispersion of Electromagnetic Particle-In-Cell Code : Finite Grid Instability

    CERN Document Server

    Meyers, M D; Zeng, Y; Yi, S A; Albright, B J

    2014-01-01

    The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the electromagnetic PIC algorithm to analyze the origin of these instabilities. We rigorously derive the faithful 3D numerical dispersion of the PIC algorithm, and then specialize to the Yee FDTD scheme. In particular, we account for the manner in which the PIC algorithm updates and samples the fields and distribution function. Temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme are also explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1D dispersion relation for a ...

  8. Extended particle-in-cell schemes for physics in ultrastrong laser fields: Review and developments.

    Science.gov (United States)

    Gonoskov, A; Bastrakov, S; Efimenko, E; Ilderton, A; Marklund, M; Meyerov, I; Muraviev, A; Sergeev, A; Surmin, I; Wallin, E

    2015-08-01

    We review common extensions of particle-in-cell (PIC) schemes which account for strong field phenomena in laser-plasma interactions. After describing the physical processes of interest and their numerical implementation, we provide solutions for several associated methodological and algorithmic problems. We propose a modified event generator that precisely models the entire spectrum of incoherent particle emission without any low-energy cutoff, and which imposes close to the weakest possible demands on the numerical time step. Based on this, we also develop an adaptive event generator that subdivides the time step for locally resolving QED events, allowing for efficient simulation of cascades. Further, we present a unified technical interface for including the processes of interest in different PIC implementations. Two PIC codes which support this interface, PICADOR and ELMIS, are also briefly reviewed.

  9. Development of a relativistic Particle In Cell code PARTDYN for linear accelerator beam transport

    Science.gov (United States)

    Phadte, D.; Patidar, C. B.; Pal, M. K.

    2017-04-01

    A relativistic Particle In Cell (PIC) code PARTDYN is developed for the beam dynamics simulation of z-continuous and bunched beams. The code is implemented in MATLAB using its MEX functionality which allows both ease of development as well higher performance similar to a compiled language like C. The beam dynamics calculations carried out by the code are compared with analytical results and with other well developed codes like PARMELA and BEAMPATH. The effect of finite number of simulation particles on the emittance growth of intense beams has been studied. Corrections to the RF cavity field expressions were incorporated in the code so that the fields could be calculated correctly. The deviations of the beam dynamics results between PARTDYN and BEAMPATH for a cavity driven in zero-mode have been discussed. The beam dynamics studies of the Low Energy Beam Transport (LEBT) using PARTDYN have been presented.

  10. The Fluid-Kinetic Particle-in-Cell Solver for Plasma Simulations

    CERN Document Server

    Markidis, Stefano; Lapenta, Giovanni; Ronnmark, Kjell; Hamrin, Maria; Meliani, Zakaria; Laure, Erwin

    2013-01-01

    A new method that solves concurrently the multi-fluid and Maxwell's equations has been developed for plasma simulations. By calculating the stress tensor in the multi-fluid momentum equation by means of computational particles moving in a self-consistent electromagnetic field, the kinetic effects are retained while solving the multi-fluid equations. The Maxwell's and multi-fluid equations are discretized implicitly in time enabling kinetic simulations over time scales typical of the fluid simulations. The fluid-kinetic Particle-in-Cell solver has been implemented in a three-dimensional electromagnetic code, and tested against the ion cyclotron resonance and magnetic reconnection problems. The new method is a promising approach for coupling fluid and kinetic methods in a unified framework.

  11. Modern Gyrokinetic Particle-In-Cell Simulation of Fusion Plasmas on Top Supercomputers

    CERN Document Server

    Wang, Bei; Tang, William; Ibrahim, Khaled; Madduri, Kamesh; Williams, Samuel; Oliker, Leonid

    2015-01-01

    The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utilization of modern parallel computer architectures at the petascale and beyond. Motivated by the goal of developing a modern code capable of dealing with the physics challenge of increasing problem size with sufficient resolution, new thread-level optimizations have been introduced as well as a key additional domain decomposition. GTC-P's multiple levels of parallelism, including inter-node 2D domain decomposition and particle decomposition, as well as intra-node shared memory partition and vectorization have enabled pushing the scalability of the PIC method to extreme computational scales. In this paper, we describe the methods developed to build a highly parallelized PIC code across a broad range of supercomputer designs. This particularly includes implementations on heterogeneous systems using NVIDIA GPU accelerators and Intel Xeon...

  12. Laser-plasma interactions with a Fourier-Bessel Particle-in-Cell method

    CERN Document Server

    Andriyash, Igor A; Lifschitz, Agustin

    2016-01-01

    A new spectral particle-in-cell (PIC) method for plasma modeling is presented and discussed. In the proposed scheme, the Fourier-Bessel transform is used to translate the Maxwell equations to the quasi-cylindrical spectral domain. In this domain, the equations are solved analytically in time, and the spatial derivatives are approximated with high accuracy. In contrast to the finite-difference time domain (FDTD) methods that are commonly used in PIC, the developed method does not produce numerical dispersion, and does not involve grid staggering for the electric and magnetic fields. These features are especially valuable in modeling the wakefield acceleration of particles in plasmas. The proposed algorithm is implemented in the code PLARES-PIC, and the test simulations of laser plasma interactions are compared to the ones done with the quasi-cylindrical FDTD PIC code CALDER-CIRC.

  13. Diesel exhaust particles are mutagenic in FE1-MutaMouse lung epithelial cells

    DEFF Research Database (Denmark)

    Jacobsen, Nicklas Raun; Møller, Peter; Cohn, Corey Alexander;

    2008-01-01

    The particulate phase of diesel engine exhaust is likely carcinogenic. However, the mechanisms of diesel exhaust particles (DEPs) induced mutagenicity/carcinogenicity are still largely unknown. We determined the mutant frequency following eight repeated 72 h incubations with 37.5 or 75 microg....../ml DEP (NIST SRM 1650) in the FE1-MutaMouse lung epithelial cell line. We measured DEP-induced acellular and intracellular production of reactive oxygen species (ROS) and compared with ROS production induced by carbon black, which we have previously shown is mutagenic in this cell line [N.R. Jacobsen, A.......T. Saber, P. White, P. Moller, G. Pojana, U. Vogel, S. Loft, J. Gingerich, L. Soper, G.R. Douglas, H. Wallin. Increased mutant frequency by carbon black, but not quartz, in the lacZ and cII transgenes of mutamouse lung epithelial cells, Environ. Mol. Mutagen. 48(6) (2007) 451-461]. The mutant frequency...

  14. A Volume-Weighting Cloud-in-Cell Model for Particle Simulation of Axially Symmetric Plasmas

    Institute of Scientific and Technical Information of China (English)

    李永东; 何锋; 刘纯亮

    2005-01-01

    A volume-weighting cloud-in-cell (VW-CIC) model is developed to implement the particle-in-cell (PIC) simulation in axially symmetric systems. This model gives a first-order accuracy in the cylindrical system, and it is incorporated into a PIC code. A planar diode with a finite-radius circular emitter is simulated with the code. The simulation results show that the VW-CIC model has a better accuracy and a lower noise than the conventional area-weighting cloud-in-cell (AW-CIC) model, especially on those points near the axis. The two-dimensional (2-D) space-charge-limited current density obtained from VW-CIC model is in better agreement with Lau's analytical result. This model is more suitable for 2.5-D PIC simulation of axially symmetric plasmas.

  15. Production of CCHF Virus-Like Particle by a Baculovirus-Insect Cell Expression System

    Institute of Scientific and Technical Information of China (English)

    Zhao-rui Zhou; Man-li Wang; Fei Deng; Tian-xian Li; Zhi-hong Hu; Hua-fin Wang

    2011-01-01

    Crimean-Congo Haemorrhagic Fever Virus(CCHFV)is a tick-born virus of the Nairovirus genus within the Bunyaviridae family,which is widespread and causes,high fatality. The nucleocapsid of CCHFV is comprised of N proteins that are encoded by the S segment. In this research,the N protein of CCHFV was expressed in insect cells using a recombinant baculovirus. Under an electron microscope,Virus-Like Particles (VLPs)with various size and morphology were observed in cytoplasmic vesicles in the infected cells.Sucrose-gradient purification of the cell lysate indicated that the VLPs were mainly located in the upper fraction after ultracentrifugation,which was confirmed by Western blot analysis and immuno-electron microscopy(IEM).

  16. Development of the CAS-LIBB single-particle microbeam for localized irradiation of living cells

    Institute of Scientific and Technical Information of China (English)

    WANG Xufei; XU Mingliang; WU Lijun; WANG Shaohu; FENG Huiyun; ZHAN Furu; PENG Shixiang; HU Chundong; ZHANG Shuqing; CHENG Jianjun; SHI Zhongtao; WANG Xiaohua; YUAN Hang; YUAN Haitao; YU Zengliang; CHEN Lianyun; HU Zhiwen; LI Jun; WU Yu; CHEN Bin; HU Suhua; ZHANG Jun

    2004-01-01

    A single-particle microbeam facility has been constructed at the Key Laboratory of Ion Beam Bioengineering (LIBB), Chinese Academy of Sciences (CAS). The system was designed to deliver a defined numbers of hydrogen ions, produced by a van de Graaff accelerator, in an energy range of 2.0-3.0 MeV, into an area smaller than that of the nucleus of an individual living cell. The beam is collimated by a borosilicate glass capillary that forms the beam-line exit. An integrated computer program recognizes the cells and locates them one by one over the microbeam exit for irradiation. We present technical details of the CAS-LIBB microbeam facility, particularly on the collimator, hardware, control program, as well as cell irradiation protocols available. Various factors contributing to the targeting and positioning precision are discussed along with accuracy measurement results.

  17. Sulfated fucan from marine alga inhibits HeLa cells infection by HTLV-1 free particles: semi-quantitative analysis

    Directory of Open Access Journals (Sweden)

    Maria T. V. Romanos

    2011-04-01

    Full Text Available A sulfated fucan from Laminaria abyssalis marine alga prevented the interaction of HTLV-1 particles, purified from the MT-2 cell line, with HeLa cells. The infection obtained using a concentrated virus suspension was detected only by amplification of the newly synthesized HTLV-1 proviral cDNA by the nested-polymerase chain reaction (PCR. The sulfated polysaccharide was not toxic to the cells at a concentration of 100 µg/mL and prevented infection by the viral particles when added to the cell monolayers. The proviral cDNA was only detected when the sulfated polysaccharide was added to the cells three hours post-infection, indicating that the inhibitory activity occurred in the initial stages of virus-cell interaction. Our results demonstrate, for the first time, the ability of a sulfated fucan from marine algae to inhibit virus transmission through free virus particles.

  18. ISDD: A computational model of particle sedimentation, diffusion and target cell dosimetry for in vitro toxicity studies

    Directory of Open Access Journals (Sweden)

    Chrisler William B

    2010-11-01

    Full Text Available Abstract Background The difficulty of directly measuring cellular dose is a significant obstacle to application of target tissue dosimetry for nanoparticle and microparticle toxicity assessment, particularly for in vitro systems. As a consequence, the target tissue paradigm for dosimetry and hazard assessment of nanoparticles has largely been ignored in favor of using metrics of exposure (e.g. μg particle/mL culture medium, particle surface area/mL, particle number/mL. We have developed a computational model of solution particokinetics (sedimentation, diffusion and dosimetry for non-interacting spherical particles and their agglomerates in monolayer cell culture systems. Particle transport to cells is calculated by simultaneous solution of Stokes Law (sedimentation and the Stokes-Einstein equation (diffusion. Results The In vitro Sedimentation, Diffusion and Dosimetry model (ISDD was tested against measured transport rates or cellular doses for multiple sizes of polystyrene spheres (20-1100 nm, 35 nm amorphous silica, and large agglomerates of 30 nm iron oxide particles. Overall, without adjusting any parameters, model predicted cellular doses were in close agreement with the experimental data, differing from as little as 5% to as much as three-fold, but in most cases approximately two-fold, within the limits of the accuracy of the measurement systems. Applying the model, we generalize the effects of particle size, particle density, agglomeration state and agglomerate characteristics on target cell dosimetry in vitro. Conclusions Our results confirm our hypothesis that for liquid-based in vitro systems, the dose-rates and target cell doses for all particles are not equal; they can vary significantly, in direct contrast to the assumption of dose-equivalency implicit in the use of mass-based media concentrations as metrics of exposure for dose-response assessment. The difference between equivalent nominal media concentration exposures on a

  19. Effects of ultrafine particles-induced oxidative stress on Clara cells in allergic lung inflammation

    Science.gov (United States)

    2010-01-01

    Background Clara cell protein (CC16), the main secretory product of bronchiolar Clara cells, plays an important protective role in the respiratory tract against oxidative stress and inflammation. The purpose of the study was to investigate the role of elemental carbon ultrafine particles (EC-UFP)-induced oxidative stress on Clara cells and CC16 in a mouse model of allergic lung inflammation. Methods Ovalbumin (OVA)-sensitized mice were exposed to EC-UFP (507 μg/m3 for 24 h) or filtered air immediately prior to allergen challenge and systemically treated with N-acetylcysteine (NAC) or vehicle prior and during EC-UFP inhalation. CC16 was measured up to one week after allergen challenge in bronchoalveolar lavage fluid (BALF) and in serum. The relative expression of CC16 and TNF-α mRNA were measured in lung homogenates. A morphometrical analysis of mucus hypersecretion and electron microscopy served to investigate goblet cell metaplasia and Clara cell morphological alterations. Results In non sensitized mice EC-UFP inhalation caused alterations in CC16 concentration, both at protein and mRNA level, and induced Clara cell hyperplasia. In sensitized mice, inhalation of EC-UFP prior to OVA challenge caused most significant alterations of BALF and serum CC16 concentration, BALF total protein and TNF-α relative expression compared to relevant controls; their Clara cells displayed the strongest morphological alterations and strongest goblet cell metaplasia occurred in the small airways. NAC strongly reduced both functional and morphological alterations of Clara cells. Conclusion Our findings demonstrate that oxidative stress plays an important role in EC-UFP-induced augmentation of functional and morphological alterations of Clara cells in allergic lung inflammation. PMID:20420656

  20. Effects of ultrafine particles-induced oxidative stress on Clara cells in allergic lung inflammation.

    Science.gov (United States)

    Alessandrini, Francesca; Weichenmeier, Ingrid; van Miert, Erik; Takenaka, Shinji; Karg, Erwin; Blume, Cornelia; Mempel, Martin; Schulz, Holger; Bernard, Alfred; Behrendt, Heidrun

    2010-04-26

    Clara cell protein (CC16), the main secretory product of bronchiolar Clara cells, plays an important protective role in the respiratory tract against oxidative stress and inflammation. The purpose of the study was to investigate the role of elemental carbon ultrafine particles (EC-UFP)-induced oxidative stress on Clara cells and CC16 in a mouse model of allergic lung inflammation. Ovalbumin (OVA)-sensitized mice were exposed to EC-UFP (507 microg/m(3) for 24 h) or filtered air immediately prior to allergen challenge and systemically treated with N-acetylcysteine (NAC) or vehicle prior and during EC-UFP inhalation. CC16 was measured up to one week after allergen challenge in bronchoalveolar lavage fluid (BALF) and in serum. The relative expression of CC16 and TNF-alpha mRNA were measured in lung homogenates. A morphometrical analysis of mucus hypersecretion and electron microscopy served to investigate goblet cell metaplasia and Clara cell morphological alterations. In non sensitized mice EC-UFP inhalation caused alterations in CC16 concentration, both at protein and mRNA level, and induced Clara cell hyperplasia. In sensitized mice, inhalation of EC-UFP prior to OVA challenge caused most significant alterations of BALF and serum CC16 concentration, BALF total protein and TNF-alpha relative expression compared to relevant controls; their Clara cells displayed the strongest morphological alterations and strongest goblet cell metaplasia occurred in the small airways. NAC strongly reduced both functional and morphological alterations of Clara cells. Our findings demonstrate that oxidative stress plays an important role in EC-UFP-induced augmentation of functional and morphological alterations of Clara cells in allergic lung inflammation.

  1. Parametric study of the vibration-induced repulsion or attraction force on a particle in a viscous fluid cell.

    Science.gov (United States)

    Saadatmand, Mehrrad; Kawaji, Masahiro

    2014-04-01

    Experiments and three-dimensional direct numerical simulations were performed to investigate the effects of physical parameters on the repulsion or attraction force affecting the motion of a particle oscillating near a solid wall of a fluid cell under microgravity. The following physical parameters were investigated: fluid cell amplitude, fluid and particle densities, angular frequency of the cell vibration, initial distance between the particle centroid and the closest cell wall, particle radius, and dynamic viscosity. Based on the simulations, a nondimensional relation was developed to relate those physical parameters to the repulsion or attraction force affecting the particle. The relation shows that the repulsion or attraction force is increased by the increase in the cell vibration amplitude and frequency and also the force direction would change from attraction to repulsion above a threshold fluid viscosity. Relations to other physical parameters were also studied and are reported. This paper follows our previous work on the physical mechanism of observed repulsion force on a particle in a viscous fluid cell [M. Saadatmand and M. Kawaji, Phys. Rev. E 88, 023019 (2013)].

  2. Selective particle and cell capture in a continuous flow using micro-vortex acoustic streaming.

    Science.gov (United States)

    Collins, David J; Khoo, Bee Luan; Ma, Zhichao; Winkler, Andreas; Weser, Robert; Schmidt, Hagen; Han, Jongyoon; Ai, Ye

    2017-05-16

    Acoustic streaming has emerged as a promising technique for refined microscale manipulation, where strong rotational flow can give rise to particle and cell capture. In contrast to hydrodynamically generated vortices, acoustic streaming is rapidly tunable, highly scalable and requires no external pressure source. Though streaming is typically ignored or minimized in most acoustofluidic systems that utilize other acoustofluidic effects, we maximize the effect of acoustic streaming in a continuous flow using a high-frequency (381 MHz), narrow-beam focused surface acoustic wave. This results in rapid fluid streaming, with velocities orders of magnitude greater than that of the lateral flow, to generate fluid vortices that extend the entire width of a 400 μm wide microfluidic channel. We characterize the forces relevant for vortex formation in a combined streaming/lateral flow system, and use these acoustic streaming vortices to selectively capture 2 μm from a mixed suspension with 1 μm particles and human breast adenocarcinoma cells (MDA-231) from red blood cells.

  3. Modeling particle-induced electron emission in a simplified plasma Test Cell

    Energy Technology Data Exchange (ETDEWEB)

    Giuliano, Paul N.; Boyd, Iain D. [Department of Aerospace Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    2013-03-21

    Particle-induced electron emission (PIE) is modeled in a simplified, well-characterized plasma Test Cell operated at UCLA. In order for PIE to be a useful model in this environment, its governing equations are first reduced to lower-order models which can be implemented in a direct simulation Monte Carlo and Particle-in-Cell framework. These reduced-order models are described in full and presented as semi-empirical models. The models are implemented to analyze the interaction of low- and high-energy ({approx}1-2 keV) xenon ions and atoms with the stainless steel electrodes of the Test Cell in order to gain insight into the emission and transport of secondary electrons. Furthermore, there is a lack of data for xenon-stainless steel atom- and ion-surface interactions for similar environments. Using experimental data as a reference, both total yields and emitted electron energy distribution functions can be deduced by observing sensitivities of current collection results to these numerical models and their parameters.

  4. Flow bioreactor design for quantitative measurements over endothelial cells using micro-particle image velocimetry

    Science.gov (United States)

    Leong, Chia Min; Voorhees, Abram; Nackman, Gary B.; Wei, Timothy

    2013-04-01

    Mechanotransduction in endothelial cells (ECs) is a highly complex process through which cells respond to changes in hemodynamic loading by generating biochemical signals involving gene and protein expression. To study the effects of mechanical loading on ECs in a controlled fashion, different in vitro devices have been designed to simulate or replicate various aspects of these physiological phenomena. This paper describes the design, use, and validation of a flow chamber which allows for spatially and temporally resolved micro-particle image velocimetry measurements of endothelial surface topography and stresses over living ECs immersed in pulsatile flow. This flow chamber also allows the study of co-cultures (i.e., ECs and smooth muscle cells) and the effect of different substrates (i.e., coverslip and/or polyethylene terepthalate (PET) membrane) on cellular response. In this report, the results of steady and pulsatile flow on fixed endothelial cells seeded on PET membrane and coverslip, respectively, are presented. Surface topography of ECs is computed from multiple two-dimensional flow measurements. The distributions of shear stress and wall pressure on each individual cell are also determined and the importance of both types of stress in cell remodeling is highlighted.

  5. Particle-based modeling effect of shape transform of single sickle red blood cells

    Science.gov (United States)

    Yang, Jun; Karniadakis, George; Dao, Ming

    2016-11-01

    Sickle red blood cells often exhibit various sickled shapes as well as higher shear and bending stiffness. To study the membrane biomechanical properties related to cell morphology, we employed multiscale coarse grain models based on dissipative particle dynamics (DPD). Through the proper orthogonal decomposition (POD) we analyst the membrane fluctuation of a single cell which probe the membrane mechanical properties. In this work, the membrane mechanics alteration caused by cell volume and surface area variation are tested. We verified that with same ratio of surface area and volume, volume differences will not affect the membrane fluctuation. We also found that by expanding the whole cell the membrane fluctuation performance does not change. To further quantify the pure shape effects, we generate cells with different aspect ratio of major axis and minor axis at which membrane exhibit different fluctuation indicating the mechanical properties divergence. Through the spatial-temporal autocorrelation of membrane fluctuations characteristics, the membrane bending stiffness and shear modulus are carefully calibrated against QPI experimental data.

  6. Flow bioreactor design for quantitative measurements over endothelial cells using micro-particle image velocimetry.

    Science.gov (United States)

    Leong, Chia Min; Voorhees, Abram; Nackman, Gary B; Wei, Timothy

    2013-04-01

    Mechanotransduction in endothelial cells (ECs) is a highly complex process through which cells respond to changes in hemodynamic loading by generating biochemical signals involving gene and protein expression. To study the effects of mechanical loading on ECs in a controlled fashion, different in vitro devices have been designed to simulate or replicate various aspects of these physiological phenomena. This paper describes the design, use, and validation of a flow chamber which allows for spatially and temporally resolved micro-particle image velocimetry measurements of endothelial surface topography and stresses over living ECs immersed in pulsatile flow. This flow chamber also allows the study of co-cultures (i.e., ECs and smooth muscle cells) and the effect of different substrates (i.e., coverslip and∕or polyethylene terepthalate (PET) membrane) on cellular response. In this report, the results of steady and pulsatile flow on fixed endothelial cells seeded on PET membrane and coverslip, respectively, are presented. Surface topography of ECs is computed from multiple two-dimensional flow measurements. The distributions of shear stress and wall pressure on each individual cell are also determined and the importance of both types of stress in cell remodeling is highlighted.

  7. The Fate of a Normal Human Cell Traversed by a Single Charged Particle

    Science.gov (United States)

    Fournier, C.; Zahnreich, S.; Kraft, D.; Friedrich, T.; Voss, K.-O.; Durante, M.; Ritter, S.

    2012-01-01

    The long-term “fate” of normal human cells after single hits of charged particles is one of the oldest unsolved issues in radiation protection and cellular radiobiology. Using a high-precision heavy-ion microbeam we could target normal human fibroblasts with exactly one or five carbon ions and measured the early cytogenetic damage and the late behaviour using single-cell cloning. Around 70% of the first cycle cells presented visible aberrations in mFISH after a single ion traversal, and about 5% of the cells were still able to form colonies. In one third of selected high-proliferative colonies we observed clonal (radiation-induced) aberrations. Terminal differentiation and markers of senescence (PCNA, p16) in the descendants of cells traversed by one carbon ion occurred earlier than in controls, but no evidence of radiation-induced chromosomal instability was found. We conclude that cells surviving single-ion traversal, often carrying clonal chromosome aberrations, undergo accelerated senescence but maintain chromosomal stability. PMID:22966418

  8. Uncovering homo-and hetero-interactions on the cell membrane using single particle tracking approaches

    Science.gov (United States)

    Torreno-Pina, Juan A.; Manzo, Carlo; Garcia-Parajo, Maria F.

    2016-03-01

    The plasma membrane of eukaryotic cells is responsible for a myriad of functions that regulate cell physiology and plays a crucial role in a multitude of processes that include adhesion, migration, signaling recognition and cell-cell communication. This is accomplished by specific interactions between different membrane components such as lipids and proteins on the lipid bilayer but also through interactions with the underlying cortical actin cytoskeleton on the intracellular side and the glycocalyx matrix in close proximity to the extracellular side. Advanced biophysical techniques, including single particle tracking (SPT) have revealed that the lateral diffusion of molecular components on the plasma membrane represents a landmark manifestation of such interactions. Indeed, by studying changes in the diffusivity of individual membrane molecules, including sub-diffusion, confined diffusion and/or transient arrest of molecules in membrane compartments, it has been possible to gain insight on the nature of molecular interactions and to infer on its functional role for cell response. In this review, we will revise some exciting results where SPT has been crucial to reveal homo- and hetero-interactions on the cell membrane.

  9. Sulfated fucan from marine alga inhibits HeLa cells infection by HTLV-1 free particles: semi-quantitative analysis

    OpenAIRE

    Romanos,Maria T. V.; Maria J. Andrada-Serpa; Mourão, Paulo A. S.; Yocie Yoneshigue-Valentin; Pereira,Mariana S.; Norma Santos; Marcia D. Wigg

    2011-01-01

    A sulfated fucan from Laminaria abyssalis marine alga prevented the interaction of HTLV-1 particles, purified from the MT-2 cell line, with HeLa cells. The infection obtained using a concentrated virus suspension was detected only by amplification of the newly synthesized HTLV-1 proviral cDNA by the nested-polymerase chain reaction (PCR). The sulfated polysaccharide was not toxic to the cells at a concentration of 100 µg/mL and prevented infection by the viral particles when added to the cell...

  10. The Plasma Simulation Code: A modern particle-in-cell code with patch-based load-balancing

    Science.gov (United States)

    Germaschewski, Kai; Fox, William; Abbott, Stephen; Ahmadi, Narges; Maynard, Kristofor; Wang, Liang; Ruhl, Hartmut; Bhattacharjee, Amitava

    2016-08-01

    This work describes the Plasma Simulation Code (PSC), an explicit, electromagnetic particle-in-cell code with support for different order particle shape functions. We review the basic components of the particle-in-cell method as well as the computational architecture of the PSC code that allows support for modular algorithms and data structure in the code. We then describe and analyze in detail a distinguishing feature of PSC: patch-based load balancing using space-filling curves which is shown to lead to major efficiency gains over unbalanced methods and a previously used simpler balancing method.

  11. Hamiltonian particle-in-cell methods for Vlasov-Maxwell equations

    CERN Document Server

    He, Yang; Qin, Hong; Liu, Jian

    2016-01-01

    In this paper, we develop Hamiltonian particle-in-cell methods for Vlasov-Maxwell equations by applying conforming finite element methods in space and splitting methods in time. For the spatial discretisation, the criteria for choosing finite element spaces are presented such that the semi-discrete system possesses a discrete non-canonical Poisson structure. We apply a Hamiltonian splitting method to the semi-discrete system in time, then the resulting algorithm is Poisson preserving and explicit. The conservative properties of the algorithm guarantee the efficient and accurate numerical simulation of the Vlasov-Maxwell equations over long-time.

  12. A spectral, quasi-cylindrical and dispersion-free Particle-In-Cell algorithm

    CERN Document Server

    Lehe, Remi; Andriyash, Igor A; Godfrey, Brendan B; Vay, Jean-Luc

    2015-01-01

    We propose a spectral Particle-In-Cell (PIC) algorithm that is based on the combination of a Hankel transform and a Fourier transform. For physical problems that have close-to-cylindrical symmetry, this algorithm can be much faster than full 3D PIC algorithms. In addition, unlike standard finite-difference PIC codes, the proposed algorithm is free of numerical dispersion. This algorithm is benchmarked in several situations that are of interest for laser-plasma interactions. These benchmarks show that it avoids a number of numerical artifacts, that would otherwise affect the physics in a standard PIC algorithm - including the zero-order numerical Cherenkov effect.

  13. Particle-in-cell modeling of gas-confined barrier discharge

    Science.gov (United States)

    Levko, Dmitry; Raja, Laxminarayan L.

    2016-04-01

    Gas-confined barrier discharge is studied using the one-dimensional Particle-in-Cell Monte Carlo Collisions model for the conditions reported by Guerra-Garcia and Martinez-Sanchez [Appl. Phys. Lett. 106, 041601 (2015)]. Depending on the applied voltage, two modes of discharge are observed. In the first mode, the discharge develops in the entire interelectrode gap. In the second mode, the discharge is ignited and develops only in the gas layer having smaller breakdown voltage. The one-dimensional model shows that for the conditions considered, there is no streamer stage of breakdown as is typical for a traditional dielectric barrier discharge.

  14. Thrust calculation of electric solar wind sail by particle-in-cell simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hoshi, Kento [Kyoto Univ. (Japan). Dept. of Electrical Engineering; Kojima, Hirotsugu; Yamakawa, Hiroshi [Kyoto Univ. (Japan). Research Inst. for Sustainable Humanosphere; Muranaka, Takanobu [Chukyo Univ., Nagoya (Japan). Dept. of Electrical Engineering

    2016-07-01

    In this study, thrust characteristics of an electric solar wind sail were numerically evaluated using full threedimensional particle-in-cell (PIC) simulation. The thrust obtained from the PIC simulation was lower than the thrust estimations obtained in previous studies. The PIC simulation indicated that ambient electrons strongly shield the electrostatic potential of the tether of the sail, and the strong shield effect causes a greater thrust reduction than has been obtained in previous studies. Additionally, previous expressions of the thrust estimation were modified by using the shielded potential structure derived from the present simulation results. The modified thrust estimation agreed very well with the thrust obtained from the PIC simulation.

  15. Particle-in-cell modeling of gas-confined barrier discharge

    Energy Technology Data Exchange (ETDEWEB)

    Levko, Dmitry; Raja, Laxminarayan L. [Department of Aerospace Engineering and Engineering Mechanics, The University of Texas at Austin, Austin, Texas 78712 (United States)

    2016-04-15

    Gas-confined barrier discharge is studied using the one-dimensional Particle-in-Cell Monte Carlo Collisions model for the conditions reported by Guerra-Garcia and Martinez-Sanchez [Appl. Phys. Lett. 106, 041601 (2015)]. Depending on the applied voltage, two modes of discharge are observed. In the first mode, the discharge develops in the entire interelectrode gap. In the second mode, the discharge is ignited and develops only in the gas layer having smaller breakdown voltage. The one-dimensional model shows that for the conditions considered, there is no streamer stage of breakdown as is typical for a traditional dielectric barrier discharge.

  16. Nonequilibrium Gyrokinetic Fluctuation Theory and Sampling Noise in Gyrokinetic Particle-in-cell Simulations

    Energy Technology Data Exchange (ETDEWEB)

    John A. Krommes

    2007-10-09

    The present state of the theory of fluctuations in gyrokinetic GK plasmas and especially its application to sampling noise in GK particle-in-cell PIC simulations is reviewed. Topics addressed include the Δf method, the fluctuation-dissipation theorem for both classical and GK many-body plasmas, the Klimontovich formalism, sampling noise in PIC simulations, statistical closure for partial differential equations, the theoretical foundations of spectral balance in the presence of arbitrary noise sources, and the derivation of Kadomtsev-type equations from the general formalism.

  17. Linear gyrokinetic particle-in-cell simulations for small to large toroidal wavenumbers

    Energy Technology Data Exchange (ETDEWEB)

    Fivaz, M.; Tran, T.M.; Villard, L.; Appert, K.; Brunner, S.; Vaclavik, J. [Ecole Polytechnique Federale, Lausanne (Switzerland). Centre de Recherche en Physique des Plasma (CRPP); Parker, S.E. [Colorado Univ., Boulder, CO (United States). Dept. of Physics

    1996-09-01

    We study here low frequency electrostatic microinstabilities driven by ion temperature gradients (ITG instabilities) relevant to anomalous ion heat transport in tokamaks. The plasma is modelled with gyrokinetic ions and adiabatic electrons. An axisymmetric equilibrium magnetic structure is provided by the MHD equilibrium code CHEASE. The full plasma cross-section is considered in the simulation. We follow the time-evolution of electrostatic, quasineutral perturbations of a local Maxwellian equilibrium distribution function, using two different particle-in-cell (PIC) codes running on a massively parallel CRAY-T3D. (author) 4 figs., 9 refs.

  18. Motion analysis of optically trapped particles and cells using 2D Fourier analysis

    DEFF Research Database (Denmark)

    Kristensen, Martin Verner; Ahrendt, Peter; Lindballe, Thue Bjerring;

    2012-01-01

    Motion analysis of optically trapped objects is demonstrated using a simple 2D Fourier transform technique. The displacements of trapped objects are determined directly from the phase shift between the Fourier transform of subsequent images. Using end-and side-view imaging, the stiffness...... of the trap is determined in three dimensions. The Fourier transform method is simple to implement and applicable in cases where the trapped object changes shape or where the lighting conditions change. This is illustrated by tracking a fluorescent particle and a myoblast cell, with subsequent determination...

  19. Effects of Ti, PMMA, UHMWPE, and Co-Cr wear particles on differentiation and functions of bone marrow stromal cells.

    Science.gov (United States)

    Jiang, Yunpeng; Jia, Tanghong; Gong, Weiming; Wooley, Paul H; Yang, Shang-You

    2013-10-01

    This study investigates the roles of orthopedic biomaterial particles [Ti-alloy, poly(methyl methacrylate) (PMMA), ultrahigh-molecular-weight polyethylene (UHMWPE), Co-Cr alloy] on the differentiation and functions of bone marrow stromal cells (BMSCs). Cells were isolated from femurs of BALB/c mice and cultured in complete osteoblast-induction medium in presence of micron-sized biomaterial particles at various doses. 3-(4,5)-Dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay and lactate dehydrogenase assay were performed for cell proliferation and cytotoxicity. Differentiation and function of osteoblasts were evaluated by alkaline phosphatase (ALP), osteocalcin, RANKL, OSX, and Runx2 expressions. Murine interleukin-1 (IL-1), IL-6, and tumor necrosis factor-α in culture media were determined by enzyme-linked immunosorbent assay. Challenge with low doses of Ti, UHMWPE, or Co-Cr particles markedly promoted the bone marrow cell proliferation while high dose of Co-Cr significantly inhibited cell growth (p UHMWPE particles (0.63 mg/mL) exhibited strong ALP activity, whereas Ti and Co-Cr groups showed minimal effects (p UHMWPE and Ti particles also promoted higher expression of proinflammatory cytokines. Real-time polymerase chain reaction data suggested that cells treated with low dose (0.5 mg/mL) particles resulted in distinctly diminished RANKL expression compared to those exposed to high concentrated (3 mg/mL) particles. In conclusion, various types of wear debris particles behaved differently in the differentiation, maturation, and functions of osteogenic cells; and the particulate debris-interacted BMSCs may play an important role in the pathogenesis and process of the debris-associated aseptic prosthetic loosening.

  20. Fabrication of dye-sensitized solar cell (DSSC) using different particle sizes of TiO2 deposited via nano-particle deposition system (NPDS).

    Science.gov (United States)

    Kim, Yang-Hee; Kim, Kwang-Su; Lee, Jin-Woong; Kim, Min-Saeng; Choi, Jung-Oh; Ahn, Sung-Hoon; Lee, Caroline Sunyong

    2012-04-01

    TiO2 layers were fabricated using a nano-particle deposition system (NPDS) on transparent conductive oxide (TCO) glass for dye sensitized solar cells (DSSCs). Conventionally, TiO2 paste for working electrodes has been fabricated using paste type methods. The fabricated paste composed of a mixture of nano-sized TiO2 powders, binders and solutions is then painted on TCO glass. After drying, the TiO2 layer on TCO glass is sintered to make a path for electron transfer. TiO2 layers formed by this paste type method require numerous steps, which can be time consuming. In this study, TiO2 powders were sprayed directly on TCO glass using NPDS in order to simplify the fabrication steps. To improve porosity and produce scattering layers, commercial nanocrystalline TiO, powders with different sizes were alternately deposited. Moreover, powders with different sizes were mixed and deposited on the TCO glass. The results indicate that the DSSCs with a TiO2 layer composed of different particle sizes had better cell performance than the cells assembled with single-sized TiO2 particles. Therefore, this study shows that a dry TiO2 coating process is possible for DSSC fabrication to improve its cell efficiencies, and this method can easily be applied on flexible substrates since NPDS is a room-temperature deposition process.

  1. A computational framework for particle and whole cell tracking applied to a real biological dataset.

    Science.gov (United States)

    Yang, Feng Wei; Venkataraman, Chandrasekhar; Styles, Vanessa; Kuttenberger, Verena; Horn, Elias; von Guttenberg, Zeno; Madzvamuse, Anotida

    2016-05-24

    Cell tracking is becoming increasingly important in cell biology as it provides a valuable tool for analysing experimental data and hence furthering our understanding of dynamic cellular phenomena. The advent of high-throughput, high-resolution microscopy and imaging techniques means that a wealth of large data is routinely generated in many laboratories. Due to the sheer magnitude of the data involved manual tracking is often cumbersome and the development of computer algorithms for automated cell tracking is thus highly desirable. In this work, we describe two approaches for automated cell tracking. Firstly, we consider particle tracking. We propose a few segmentation techniques for the detection of cells migrating in a non-uniform background, centroids of the segmented cells are then calculated and linked from frame to frame via a nearest-neighbour approach. Secondly, we consider the problem of whole cell tracking in which one wishes to reconstruct in time whole cell morphologies. Our approach is based on fitting a mathematical model to the experimental imaging data with the goal being that the physics encoded in the model is reflected in the reconstructed data. The resulting mathematical problem involves the optimal control of a phase-field formulation of a geometric evolution law. Efficient approximation of this challenging optimal control problem is achieved via advanced numerical methods for the solution of semilinear parabolic partial differential equations (PDEs) coupled with parallelisation and adaptive resolution techniques. Along with a detailed description of our algorithms, a number of simulation results are reported on. We focus on illustrating the effectivity of our approaches by applying the algorithms to the tracking of migrating cells in a dataset which reflects many of the challenges typically encountered in microscopy data.

  2. ISDD: A Computational Model of Particle Sedimentation, Diffusion and Target Cell Dosimetry for In Vitro Toxicity Studies

    Energy Technology Data Exchange (ETDEWEB)

    Hinderliter, Paul M.; Minard, Kevin R.; Orr, Galya; Chrisler, William B.; Thrall, Brian D.; Pounds, Joel G.; Teeguarden, Justin G.

    2010-11-30

    Background: The difficulty of directly measuring cellular dose is a significant obstacle to application of target tissue dosimetry for nanoparticle and microparticle toxicity assessment. As a consequence, the target tissue paradigm for dosimetry and hazard assessment of nanoparticles has largely been ignored in favor of using metrics of exposure (e.g. μg particle/mL culture medium, particle surface area/mL, particle number/mL). We have developed a computational model of solution particokinetics (sedimentation, diffusion) and dosimetry for non-interacting spherical particles and their agglomerates in monolayer cell culture systems. Particle transport to cells is calculated by simultaneous solution of Stokes Law (sedimentation) and the Stokes-Einstein equation (diffusion). Results: The In vitro Sedimentation, Diffusion and Dosimetry model (ISDD) was tested against measured transport rates or cellular doses for multiple sizes of polystyrene spheres (20-1100 nm), 35 nm amorphous silica, and large agglomerates of 30 nm iron oxide particles. Overall, without adjusting any parameters, model predicted doses were in close agreement with the experimental data, differing from as little as 5% to as much as three-fold, but in most cases approximately two-fold, within the limits of the accuracy of the measurement systems. Applying the model, we generalize the effects of particle size, particle density, agglomeration state and agglomerate characteristics on target cell dosimetry in vitro. Conclusions: Our results confirm our hypothesis that the dose-rates for all particles are not equal, but can vary significantly, in direct contrast to the assumption of dose-equivalency implicit in the use of mass-based media concentrations as metrics of exposure for dose-response assessment. The difference between equivalent nominal media concentration exposures on a μg/mL basis and target cell doses on a particle surface area or number basis can be as high as three to six orders of magnitude

  3. A particle-based model to simulate the micromechanics of single-plant parenchyma cells and aggregates.

    Science.gov (United States)

    Van Liedekerke, P; Ghysels, P; Tijskens, E; Samaey, G; Smeedts, B; Roose, D; Ramon, H

    2010-05-26

    This paper is concerned with addressing how plant tissue mechanics is related to the micromechanics of cells. To this end, we propose a mesh-free particle method to simulate the mechanics of both individual plant cells (parenchyma) and cell aggregates in response to external stresses. The model considers two important features in the plant cell: (1) the cell protoplasm, the interior liquid phase inducing hydrodynamic phenomena, and (2) the cell wall material, a viscoelastic solid material that contains the protoplasm. In this particle framework, the cell fluid is modeled by smoothed particle hydrodynamics (SPH), a mesh-free method typically used to address problems with gas and fluid dynamics. In the solid phase (cell wall) on the other hand, the particles are connected by pairwise interactions holding them together and preventing the fluid to penetrate the cell wall. The cell wall hydraulic conductivity (permeability) is built in as well through the SPH formulation. Although this model is also meant to be able to deal with dynamic and even violent situations (leading to cell wall rupture or cell-cell debonding), we have concentrated on quasi-static conditions. The results of single-cell compression simulations show that the conclusions found by analytical models and experiments can be reproduced at least qualitatively. Relaxation tests revealed that plant cells have short relaxation times (1 micros-10 micros) compared to mammalian cells. Simulations performed on cell aggregates indicated an influence of the cellular organization to the tissue response, as was also observed in experiments done on tissues with a similar structure.

  4. Differences between real and particle-in-cell plasmas: effects of coarse-graining

    CERN Document Server

    Melzani, Mickaël; Folini, Doris; Winisdoerffer, Christophe

    2013-01-01

    The PIC model relies on two building blocks. The first stems from the capability of computers to handle only up to $\\sim10^{10}$ particles, while real plasmas contain from $10^4$ to $10^{20}$ particles per Debye sphere: a coarse-graining step must be used, whereby of the order of $p\\sim10^{10}$ real particles are represented by a single computer superparticle. The second is field storage on a grid with its subsequent finite superparticle size. We introduce the notion of coarse-graining dependent quantities, i.e. physical quantities depending on the number $p$. They all derive from the plasma parameter $\\Lambda$, which we show to be proportional to $1/p$. We explore three examples: the rapid collision- and fluctuation-induced thermalization of plasmas with different temperatures, that scale with the number of superparticles per grid cell and are a factor $p\\sim10^{10}$ faster than in real plasmas; the high level of electrostatic fluctuations in a thermal plasma, with corrections due to the finite superparticle...

  5. Multidimensional, fully implicit, exactly conserving electromagnetic particle-in-cell simulations

    Science.gov (United States)

    Chacon, Luis

    2015-09-01

    We discuss a new, conservative, fully implicit 2D-3V particle-in-cell algorithm for non-radiative, electromagnetic kinetic plasma simulations, based on the Vlasov-Darwin model. Unlike earlier linearly implicit PIC schemes and standard explicit PIC schemes, fully implicit PIC algorithms are unconditionally stable and allow exact discrete energy and charge conservation. This has been demonstrated in 1D electrostatic and electromagnetic contexts. In this study, we build on these recent algorithms to develop an implicit, orbit-averaged, time-space-centered finite difference scheme for the Darwin field and particle orbit equations for multiple species in multiple dimensions. The Vlasov-Darwin model is very attractive for PIC simulations because it avoids radiative noise issues in non-radiative electromagnetic regimes. The algorithm conserves global energy, local charge, and particle canonical-momentum exactly, even with grid packing. The nonlinear iteration is effectively accelerated with a fluid preconditioner, which allows efficient use of large timesteps, O(√{mi/me}c/veT) larger than the explicit CFL. In this presentation, we will introduce the main algorithmic components of the approach, and demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 1D and 2D. Support from the LANL LDRD program and the DOE-SC ASCR office.

  6. Global Explicit Particle-in-cell Simulations of the Nonstationary Bow Shock and Magnetosphere

    Science.gov (United States)

    Yang, Zhongwei; Huang, Can; Liu, Ying D.; Parks, George K.; Wang, Rui; Lu, Quanming; Hu, Huidong

    2016-07-01

    We carry out two-dimensional global particle-in-cell simulations of the interaction between the solar wind and a dipole field to study the formation of the bow shock and magnetosphere. A self-reforming bow shock ahead of a dipole field is presented by using relatively high temporal-spatial resolutions. We find that (1) the bow shock and the magnetosphere are formed and reach a quasi-stable state after several ion cyclotron periods, and (2) under the B z southward solar wind condition, the bow shock undergoes a self-reformation for low β i and high M A . Simultaneously, a magnetic reconnection in the magnetotail is found. For high β i and low M A , the shock becomes quasi-stationary, and the magnetotail reconnection disappears. In addition, (3) the magnetopause deflects the magnetosheath plasmas. The sheath particles injected at the quasi-perpendicular region of the bow shock can be convected downstream of an oblique shock region. A fraction of these sheath particles can leak out from the magnetosheath at the wings of the bow shock. Hence, the downstream situation is more complicated than that for a planar shock produced in local simulations.

  7. Global explicit particle-in-cell simulations of the nonstationary bow shock and magnetosphere

    CERN Document Server

    Yang, Zhongwei; Liu, Ying D; Parks, George K; Wang, Rui; Lu, Quanming; Hu, Huidong

    2016-01-01

    We carry out two-dimensional global particle-in-cell simulations of the interaction between the solar wind and a dipole field to study the formation of the bow shock and magnetosphere. A self-reforming bow shock ahead of a dipole field is presented by using relatively high temporal-spatial resolutions. We find that (1) the bow shock and the magnetosphere are formed and reach a quasi-stable state after several ion cyclotron periods, and (2) under the Bz southward solar wind condition the bow shock undergoes a self-reformation for low \\b{eta}i and high MA. Simultaneously, a magnetic reconnection in the magnetotail is found. For high \\b{eta}i and low MA, the shock becomes quasi-stationary, and the magnetotail reconnection disappears. In addition, (3) the magnetopause deflects the magnetosheath plasmas. The sheath particles injected at the quasi-perpendicular region of the bow shock can be convected to downstream of an oblique shock region. A fraction of these sheath particles can leak out from the magnetosheath ...

  8. Spacecraft charging analysis with the implicit particle-in-cell code iPic3D

    Energy Technology Data Exchange (ETDEWEB)

    Deca, J.; Lapenta, G. [Centre for Mathematical Plasma Astrophysics, KU Leuven, Celestijnenlaan 200B bus 2400, 3001 Leuven (Belgium); Marchand, R. [Department of Physics, University of Alberta, Edmonton, Alberta T6G 2J1 (Canada); Markidis, S. [High Performance Computing and Visualization Department, KTH Royal Institute of Technology, Stockholm (Sweden)

    2013-10-15

    We present the first results on the analysis of spacecraft charging with the implicit particle-in-cell code iPic3D, designed for running on massively parallel supercomputers. The numerical algorithm is presented, highlighting the implementation of the electrostatic solver and the immersed boundary algorithm; the latter which creates the possibility to handle complex spacecraft geometries. As a first step in the verification process, a comparison is made between the floating potential obtained with iPic3D and with Orbital Motion Limited theory for a spherical particle in a uniform stationary plasma. Second, the numerical model is verified for a CubeSat benchmark by comparing simulation results with those of PTetra for space environment conditions with increasing levels of complexity. In particular, we consider spacecraft charging from plasma particle collection, photoelectron and secondary electron emission. The influence of a background magnetic field on the floating potential profile near the spacecraft is also considered. Although the numerical approaches in iPic3D and PTetra are rather different, good agreement is found between the two models, raising the level of confidence in both codes to predict and evaluate the complex plasma environment around spacecraft.

  9. Adapting Particle-In-Cell simulations to the study of short pulse laser damage

    Science.gov (United States)

    Mitchell, Robert; Schumacher, Douglass; Chowdhury, Enam

    2014-10-01

    We present novel Particle-In-Cell (PIC) simulations of the full femtosecond-pulse laser damage process and the resulting damage spot morphology. At the heart of these simulations is the implementation, for the first time, of a Lennard-Jones pair potential model (LJPPM) for PIC codes. The use of PIC facilitates the first ab-initio treatment of realistic target sizes, retaining the strengths of PIC including self-consistent treatment of the laser-particle interaction and subsequent generation of plasma waves and electron heating, while the LJPPM allows a PIC code to treat a system of particles as a medium which can ablate, melt, and resolidify. Combining these two approaches, we model the effect of a femtosecond-pulse laser on metal targets near and above the damage threshold and compare to recent experimental results. In particular, we present the first simulations of the emergence of Laser-Induced Periodic Surface Structure (LIPSS) upon femtosecond-pulse laser irradiation.

  10. Parallel mesh support for particle-in-cell methods in magnetic fusion simulations

    Science.gov (United States)

    Yoon, Eisung; Shephard, Mark S.; Seol, E. Seegyoung; Kalyanaraman, Kaushik; Ibanez, Daniel

    2016-10-01

    As supercomputing power continues to increase Particle-In-Cell (PIC) methods are being widely adopted for transport simulations of magnetic fusion devices. Current implementations place a copy of the entire continuum mesh and its fields used in the PIC calculations on every node. This is in general not a scalable solution as computational power continues to grow faster than node level memory. To address this scalability issue, while still maintaining sufficient mesh per node to control costly inter-node communication, a new unstructured mesh distribution methods and associated mesh based PIC calculation procedure is being developed building on the parallel unstructured mesh infrastructure (PUMI). Key components to be outlined in the presentation include (i) the mesh distribution strategy, (ii) how the particles are tracked during a push cycle taking advantage of the unstructured mesh adjacency structures and searches based on that structure, and (iii) how the field solve steps and particle migration are controlled. Performance comparisons to the current approach will also be presented.

  11. Relativistic magnetic reconnection in collisionless ion-electron plasmas explored with particle-in-cell simulations

    CERN Document Server

    Melzani, Mickaël; Folini, Doris; Winisdoerffer, Christophe; Favre, Jean M

    2014-01-01

    Magnetic reconnection is a leading mechanism for magnetic energy conversion and high-energy non-thermal particle production in a variety of high-energy astrophysical objects, including ones with relativistic ion-electron plasmas (e.g., microquasars or AGNs) - a regime where first principle studies are scarce. We present 2D particle-in-cell (PIC) simulations of low $\\beta$ ion-electron plasmas under relativistic conditions, i.e., with inflow magnetic energy exceeding the plasma rest-mass energy. We identify outstanding properties: (i) For relativistic inflow magnetizations (here $10 80$), the reconnection electric field is sustained more by bulk inertia than by thermal inertia. It challenges the thermal-inertia-paradigm and its implications. (iii) The inflows feature sharp transitions at the entrance of the diffusion zones. These are not shocks but results from particle ballistic motions, all bouncing at the same location, provided that the thermal velocity in the inflow is far smaller than the inflow E cross...

  12. Particle size and surface charge affect particle uptake by human dendritic cells in an in vitro model

    DEFF Research Database (Denmark)

    Foged, Camilla; Brodin, Birger; Frøkjær, Sven;

    2005-01-01

    Current vaccine development includes optimization of antigen delivery to antigen presenting cells, such as dendritic cells (DC). Particulate systems have attracted increasing attention in the development of vaccine delivery systems. In the present study, we investigated DC uptake of model...

  13. Fe3O4/BSA particles induce osteogenic differentiation of mesenchymal stem cells under static magnetic field.

    Science.gov (United States)

    Jiang, Pengfei; Zhang, Yixian; Zhu, Chaonan; Zhang, Wenjing; Mao, Zhengwei; Gao, Changyou

    2016-12-01

    Differentiation of stem cells is influenced by many factors, yet uptake of the magnetic particles with or without magnetic field is rarely tackled. In this study, iron oxide nanoparticles-loaded bovine serum albumin (BSA) (Fe3O4/BSA) particles were prepared, which showed a spherical morphology with a diameter below 200 nm, negatively charged surface, and tunable magnetic property. The particles could be internalized into bone marrow mesenchymal stem cells (MSCs), and their release from the cells was significantly retarded under external magnetic field, resulting in almost twice intracellular amount of the particles within 21 d compared to that of the magnetic field free control. Uptake of the Fe3O4/BSA particles enhanced significantly the osteogenic differentiation of MSCs under a static magnetic field, as evidenced by elevated alkaline phosphatase (ALP) activity, calcium deposition, and expressions of collagen type I and osteocalcin at both mRNA and protein levels. Therefore, uptake of the Fe3O4/BSA particles brings significant influence on the differentiation of MSCs under magnetic field, and thereby should be paid great attention for practical applications. Differentiation of stem cells is influenced by many factors, yet uptake of the magnetic particles with or without magnetic field is rarely tackled. In this study, iron oxide nanoparticles-loaded bovine serum albumin (BSA) (Fe3O4/BSA) particles with a diameter below 200nm, negatively charged surface, tunable Fe3O4 content and subsequently adjustable magnetic property were prepared. The particles could be internalized into bone marrow mesenchymal stem cells (MSCs), and their release from the cells was significantly retarded under external magnetic field. Uptake of the Fe3O4/BSA particles enhanced significantly the osteogenic differentiation of MSCs under a constant static magnetic field, while the magnetic particles and external magnetic field alone do not influence significantly the osteogenic differentiation

  14. Low doses of alpha particles do not induce sister chromatid exchanges in bystander Chinese hamster cells defective in homologous recombination

    Energy Technology Data Exchange (ETDEWEB)

    Nagasawa, H; Wilson, P F; Chen, D J; Thompson, L H; Bedford, J S; Little, J B

    2007-10-26

    We reported previously that the homologous recombinational repair (HRR)-deficient Chinese hamster mutant cell line irs3 (deficient in the Rad51 paralog Rad51C) showed only a 50% spontaneous frequency of sister chromatid exchange (SCE) as compared to parental wild-type V79 cells. Furthermore, when irradiated with very low doses of alpha particles, SCEs were not induced in irs3 cells, as compared to a prominent bystander effect observed in V79 cells (Nagasawa et al., Radiat. Res. 164, 141-147, 2005). In the present study, we examined additional Chinese hamster cell lines deficient in the Rad51 paralogs Rad51C, Rad51D, Xrcc2, and Xrcc3 as well as another essential HRR protein, Brca2. Spontaneous SCE frequencies in non-irradiated wild-type cell lines CHO, AA8 and V79 were 0.33 SCE/chromosome, whereas two Rad51C-deficient cell lines showed only 0.16 SCE/chromosome. Spontaneous SCE frequencies in cell lines defective in Rad51D, Xrcc2, Xrcc3, and Brca2 ranged from 0.23-0.33 SCE/chromosome, 0-30% lower than wild-type cells. SCEs were induced significantly 20-50% above spontaneous levels in wild-type cells exposed to a mean dose of 1.3 mGy of alpha particles (<1% of nuclei traversed by an alpha particle). However, induction of SCEs above spontaneous levels was minimal or absent after {alpha}-particle irradiation in all of the HRR-deficient cell lines. These data suggest that Brca2 and the Rad51 paralogs contribute to DNA damage repair processes induced in bystander cells (presumably oxidative damage repair in S-phase cells) following irradiation with very low doses of alpha particles.

  15. Delivery of differentiation factors by mesoporous silica particles assists advanced differentiation of transplanted murine embryonic stem cells

    DEFF Research Database (Denmark)

    Garcia-Bennett, Alfonso E; Kozhevnikova, Mariya; König, Niclas;

    2013-01-01

    Stem cell transplantation holds great hope for the replacement of damaged cells in the nervous system. However, poor long-term survival after transplantation and insufficiently robust differentiation of stem cells into specialized cell types in vivo remain major obstacles for clinical application...... neurotrophic factor and glial cell line-derived neurotrophic factor, respectively, with these particles enabled not only robust functional differentiation of motor neurons from transplanted embryonic stem cells but also their long-term survival in vivo. We propose that the delivery of growth factors...... by mesoporous nanoparticles is a potentially versatile and widely applicable strategy for efficient differentiation and functional integration of stem cell derivatives upon transplantation....

  16. Tracking the virus-like particles of Macrobrachium rosenbergii nodavirus in insect cells

    Science.gov (United States)

    Hanapi, Ummi Fairuz; Yong, Chean Yeah; Goh, Zee Hong; Alitheen, Noorjahan Banu; Yeap, Swee Keong

    2017-01-01

    Macrobrachium rosenbergii nodavirus (MrNv) poses a major threat to the prawn industry. Currently, no effective vaccine and treatment are available to prevent the spread of MrNv. Its infection mechanism and localisation in a host cell are also not well characterised. The MrNv capsid protein (MrNvc) produced in Escherichia coli self-assembled into virus-like particles (VLPs) resembling the native virus. Thus, fluorescein labelled MrNvc VLPs were employed as a model to study the virus entry and localisation in Spodoptera frugiperda, Sf9 cells. Through fluorescence microscopy and sub-cellular fractionation, the MrNvc was shown to enter Sf9 cells, and eventually arrived at the nucleus. The presence of MrNvc within the cytoplasm and nucleus of Sf9 cells was further confirmed by the Z-stack imaging. The presence of ammonium chloride (NH4Cl), genistein, methyl-β-cyclodextrin or chlorpromazine (CPZ) inhibited the entry of MrNvc into Sf9 cells, but cytochalasin D did not inhibit this process. This suggests that the internalisation of MrNvc VLPs is facilitated by caveolae- and clathrin-mediated endocytosis. The whole internalisation process of MrNvc VLPs into a Sf9 cell was recorded with live cell imaging. We have also identified a potential nuclear localisation signal (NLS) of MrNvc through deletion mutagenesis and verified by classical-NLS mapping. Overall, this study provides an insight into the journey of MrNvc VLPs in insect cells. PMID:28194311

  17. Tracking the virus-like particles of Macrobrachium rosenbergii nodavirus in insect cells

    Directory of Open Access Journals (Sweden)

    Ummi Fairuz Hanapi

    2017-02-01

    Full Text Available Macrobrachium rosenbergii nodavirus (MrNv poses a major threat to the prawn industry. Currently, no effective vaccine and treatment are available to prevent the spread of MrNv. Its infection mechanism and localisation in a host cell are also not well characterised. The MrNv capsid protein (MrNvc produced in Escherichia coli self-assembled into virus-like particles (VLPs resembling the native virus. Thus, fluorescein labelled MrNvc VLPs were employed as a model to study the virus entry and localisation in Spodoptera frugiperda, Sf9 cells. Through fluorescence microscopy and sub-cellular fractionation, the MrNvc was shown to enter Sf9 cells, and eventually arrived at the nucleus. The presence of MrNvc within the cytoplasm and nucleus of Sf9 cells was further confirmed by the Z-stack imaging. The presence of ammonium chloride (NH4Cl, genistein, methyl-β-cyclodextrin or chlorpromazine (CPZ inhibited the entry of MrNvc into Sf9 cells, but cytochalasin D did not inhibit this process. This suggests that the internalisation of MrNvc VLPs is facilitated by caveolae- and clathrin-mediated endocytosis. The whole internalisation process of MrNvc VLPs into a Sf9 cell was recorded with live cell imaging. We have also identified a potential nuclear localisation signal (NLS of MrNvc through deletion mutagenesis and verified by classical-NLS mapping. Overall, this study provides an insight into the journey of MrNvc VLPs in insect cells.

  18. In vitro toxicity of nanosized copper particles in PC12 cells induced by oxidative stress

    Energy Technology Data Exchange (ETDEWEB)

    Xu Pengjuan; Xu Jing; Liu Shichang [Nankai University, College of Medicine (China); Ren, Guogang [University of Hertfordshire, School of Aerospace Engineering (United Kingdom); Yang Zhuo, E-mail: zhuoyang@nankai.edu.cn [Nankai University, College of Medicine (China)

    2012-06-15

    Recent evidence suggests that some nanomaterials, which are widely used in many fields, have health effects. In order to investigate the cytotoxicity induced by nanosized copper particles (nano-Cu), PC12 cells, which were widely used as an in vitro model for the neuron research, were treated with different concentrations (0, 1, 10, 30, and 100 {mu}g/mL) of nano-Cu. The cell viability was determined by measurement of the reduction product of 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT). The oxidative stress induced by nano-Cu and its possible mechanism were studied in relation to the generation of reactive oxygen species (ROS) and the cellular activity of superoxide dismutase (SOD). Results showed that incubation of PC12 cells with increasing concentrations of nano-Cu induced a decrease of cell viability in a concentration- and time-dependent manner. In addition, flow cytometry assay using Annexin V-FITC/PI staining was used to investigate the mode of nano-Cu-induced cell death and quantified the percentage of apoptotic cells. Results showed that nano-Cu induced the significant apoptosis in PC12 cells. Meanwhile, intracellular accumulation of ROS was increased with the increased concentrations of nano-Cu and it was associated with decreased SOD activity, which was probably due to protect effects against the oxidative stress in PC12 cells. Results suggested that both excessive intracellular ROS and decreased SOD contributed to nano-Cu-induced cytotoxicity. In other words, the increasing of oxidative stress was a key mechanism in PC12 apoptosis induced by nano-Cu.

  19. Microfluidic Adaptation of Density-Gradient Centrifugation for Isolation of Particles and Cells

    Directory of Open Access Journals (Sweden)

    Yuxi Sun

    2017-08-01

    Full Text Available Density-gradient centrifugation is a label-free approach that has been extensively used for cell separations. Though elegant, this process is time-consuming (>30 min, subjects cells to high levels of stress (>350 g and relies on user skill to enable fractionation of cells that layer as a narrow band between the density-gradient medium and platelet-rich plasma. We hypothesized that microfluidic adaptation of this technique could transform this process into a rapid fractionation approach where samples are separated in a continuous fashion while being exposed to lower levels of stress (<100 g for shorter durations of time (<3 min. To demonstrate proof-of-concept, we designed a microfluidic density-gradient centrifugation device and constructed a setup to introduce samples and medium like Ficoll in a continuous, pump-less fashion where cells and particles can be exposed to centrifugal force and separated via different outlets. Proof-of-concept studies using binary mixtures of low-density polystyrene beads (1.02 g/cm3 and high-density silicon dioxide beads (2.2 g/cm3 with Ficoll–Paque (1.06 g/cm3 show that separation is indeed feasible with >99% separation efficiency suggesting that this approach can be further adapted for separation of cells.

  20. Replication, gene expression and particle production by a consensus Merkel Cell Polyomavirus (MCPyV genome.

    Directory of Open Access Journals (Sweden)

    Friederike Neumann

    Full Text Available Merkel Cell Polyomavirus (MCPyV genomes are clonally integrated in tumor tissues of approximately 85% of all Merkel cell carcinoma (MCC cases, a highly aggressive tumor of the skin which predominantly afflicts elderly and immunosuppressed patients. All integrated viral genomes recovered from MCC tissue or MCC cell lines harbor signature mutations in the early gene transcript encoding for the large T-Antigen (LT-Ag. These mutations selectively abrogate the ability of LT-Ag to support viral replication while still maintaining its Rb-binding activity, suggesting a continuous requirement for LT-Ag mediated cell cycle deregulation during MCC pathogenesis. To gain a better understanding of MCPyV biology, in vitro MCPyV replication systems are required. We have generated a synthetic MCPyV genomic clone (MCVSyn based on the consensus sequence of MCC-derived sequences deposited in the NCBI database. Here, we demonstrate that transfection of recircularized MCVSyn DNA into some human cell lines recapitulates efficient replication of the viral genome, early and late gene expression together with virus particle formation. However, serial transmission of infectious virus was not observed. This in vitro culturing system allows the study of viral replication and will facilitate the molecular dissection of important aspects of the MCPyV lifecycle.

  1. Effective chikungunya virus-like particle vaccine produced in insect cells.

    Directory of Open Access Journals (Sweden)

    Stefan W Metz

    Full Text Available The emerging arthritogenic, mosquito-borne chikungunya virus (CHIKV causes severe disease in humans and represents a serious public health threat in countries where Aedes spp mosquitoes are present. This study describes for the first time the successful production of CHIKV virus-like particles (VLPs in insect cells using recombinant baculoviruses. This well-established expression system is rapidly scalable to volumes required for epidemic responses and proved well suited for processing of CHIKV glycoproteins and production of enveloped VLPs. Herein we show that a single immunization with 1 µg of non-adjuvanted CHIKV VLPs induced high titer neutralizing antibody responses and provided complete protection against viraemia and joint inflammation upon challenge with the Réunion Island CHIKV strain in an adult wild-type mouse model of CHIKV disease. CHIKV VLPs produced in insect cells using recombinant baculoviruses thus represents as a new, safe, non-replicating and effective vaccine candidate against CHIKV infections.

  2. Single-particle tracking and modulation of cell entry pathways of a tetrahedral DNA nanostructure in live cells.

    Science.gov (United States)

    Liang, Le; Li, Jiang; Li, Qian; Huang, Qing; Shi, Jiye; Yan, Hao; Fan, Chunhai

    2014-07-21

    DNA is typically impermeable to the plasma membrane due to its polyanionic nature. Interestingly, several different DNA nanostructures can be readily taken up by cells in the absence of transfection agents, which suggests new opportunities for constructing intelligent cargo delivery systems from these biocompatible, nonviral DNA nanocarriers. However, the underlying mechanism of entry of the DNA nanostructures into the cells remains unknown. Herein, we investigated the endocytotic internalization and subsequent transport of tetrahedral DNA nanostructures (TDNs) by mammalian cells through single-particle tracking. We found that the TDNs were rapidly internalized by a caveolin-dependent pathway. After endocytosis, the TDNs were transported to the lysosomes in a highly ordered, microtubule-dependent manner. Although the TDNs retained their structural integrity within cells over long time periods, their localization in the lysosomes precludes their use as effective delivery agents. To modulate the cellular fate of the TDNs, we functionalized them with nuclear localization signals that directed their escape from the lysosomes and entry into the cellular nuclei. This study improves our understanding of the entry into cells and transport pathways of DNA nanostructures, and the results can be used as a basis for designing DNA-nanostructure-based drug delivery nanocarriers for targeted therapy.

  3. Controlled method of reducing electrophoretic mobility of macromolecules, particles, or cells

    Science.gov (United States)

    Vanalstine, James M. (Inventor)

    1992-01-01

    A method of reducing electrophoretic mobility of macromolecules, particles, cells, and other substances is provided which comprises interacting in a conventional electrophoretic separating procedure, the substances with a polymer-linked affinity compound comprised of a hydrophilic neutral polymer such as polyethylene glycol bound to a second component such as a hydrophobic compound, an immunocompound such as an antibody or antibody active fragment, or a ligand such as a hormone, drug, antigen, or a hapten. The reduction of electrophoretic mobility achieved is directly proportional to the concentration of the polymer-linked affinity compound employed, and such reduction can comprise up to 100 percent for particular particles and cells. The present invention is advantageous in that electrophoretic separation can now be achieved for substances whose native surface charge structure had prevented them from being separated by normal electrophoretic means. Depending on the affinity component utilized, separation can be achieved on the basis of the specific/irreversible, specific/reversible, semi-specific/reversible, relatively nonspecific/reversible, or relatively nonspecific/irreversible ligand-substance interactions.

  4. Influence of nanoporous poly(ether imide) particle extracts on human aortic endothelial cells (HAECs).

    Science.gov (United States)

    Kumar, Reddi K; Basu, Sayantani; Lemke, Horst-Dieter; Jankowski, Joachim; Kratz, Karl; Lendlein, Andreas; Tetali, Sarada D

    2016-01-01

    Accumulated uremic toxins like indoxyl sulphate, hippuric acid and p-cresyl sulphates in renal failure patients stimulate proinflammatory effects, and consequently kidney and cardiovascular diseases. Low clearance rate of these uremic toxins from the blood of uremic patients by conventional techniques like hemodialysis is due to their strong covalent albumin binding (greater than 95%) and hydrophobic nature, which led to alternatives like usage of hydrophobic adsorber's in removing these toxins from the plasma of kidney patients. Polymers like polyethylene, polyurethane, polymethylmethacrylate, cellophane and polytetrafluoroethylene were already in use as substitutes for metal devices as dialysis membranes. Among new synthetic polymers, one such ideal adsorber material are highly porous microparticles of poly(ether imide) (PEI) with diameters in the range from 50-180μm and a porosity around 88±2% prepared by a spraying and coagulation process.It is essential to make sure that these synthetic polymers should not evoke any inflammatory or apoptotic response during dialysis. Therefore in our study we evaluated in vitro effect of PEI microparticle extracts in human aortic endothelial cells (HEACs) concerning toxicity, inflammation and apoptosis. No cell toxicity was observed when HAECs were treated with PEI extracts and inflammatory/apoptotic markers were not upregulated in presence of PEI extracts. Our results ensure biocompatibility of PEI particles and further hemocompatibility of particles will be tested.

  5. From Cells to Virus Particles: Quantitative Methods to Monitor RNA Packaging

    Directory of Open Access Journals (Sweden)

    Mireia Ferrer

    2016-08-01

    Full Text Available In cells, positive strand RNA viruses, such as Retroviridae, must selectively recognize their full-length RNA genome among abundant cellular RNAs to assemble and release particles. How viruses coordinate the intracellular trafficking of both RNA and protein components to the assembly sites of infectious particles at the cell surface remains a long-standing question. The mechanisms ensuring packaging of genomic RNA are essential for viral infectivity. Since RNA packaging impacts on several essential functions of retroviral replication such as RNA dimerization, translation and recombination events, there are many studies that require the determination of RNA packaging efficiency and/or RNA packaging ability. Studies of RNA encapsidation rely upon techniques for the identification and quantification of RNA species packaged by the virus. This review focuses on the different approaches available to monitor RNA packaging: Northern blot analysis, ribonuclease protection assay and quantitative reverse transcriptase-coupled polymerase chain reaction as well as the most recent RNA imaging and sequencing technologies. Advantages, disadvantages and limitations of these approaches will be discussed in order to help the investigator to choose the most appropriate technique. Although the review was written with the prototypic simple murine leukemia virus (MLV and complex human immunodeficiency virus type 1 (HIV-1 in mind, the techniques were described in order to benefit to a larger community.

  6. Particle size- and number-dependent delivery to cells by layered double hydroxide nanoparticles.

    Science.gov (United States)

    Dong, Haiyan; Parekh, Harendra S; Xu, Zhi Ping

    2015-01-01

    It is well known that delivery efficiency to cells is highly dependent on particle size and the administered dose. However, there is a marked discrepancy in many reports, mainly due to the inconsistency in assessment of various parameters. In this particular research, we designed experiments using layered double hydroxide nanoparticles (LDH NPs) to specifically elucidate the effect of particle size, dose and dye loading manner on cellular uptake. Using the number of LDH NPs taken up by HCT-116 cells as the indicator of delivery efficiency, we found that (1) the size of sheet-like LDH in the range of 40-100 nm did not significantly affect their cellular uptake; (2) cellular uptake of 40 and 100 nm LDH NPs was increased proportionally to the number concentration below a critical value, but remained relatively constant beyond the critical value; and (3) the effect of the dye loading manner is mainly dependent on the loading capacity or yield. In particular, the loading capacity is determined by the NP specific surface area. This research may be extended to a larger size range to examine the size effect, but suggests that it is necessary to set up a protocol to evaluate the effects of NP's physicochemical properties on the cellular delivery efficiency.

  7. Composition of air pollution particles modifies oxidative stress in cells, tissues, and living systems

    Science.gov (United States)

    Epidemiological studies demonstrate an association between increased levels of ambient air pollution particles and human morbidity and mortality. Production of oxidants, either directly by the air pollution particles or by the host response to the particles, appears to be fundame...

  8. Growth of human bronchial epithelial cells at an air-liquid interface alters the response to particle exposure

    Science.gov (United States)

    Abstract: We tested the hypothesis that relative to submerged cells, airway epithelial cells grown at an air-liquid interface would have an altered response to particle exposure. RNA for IL-8, IL-6, heme oxygenase 1 and cyclooxygenase 2 increased following exposure of submer...

  9. High coating of Ru(II) complexes on gold nanoparticles for single particle luminescence imaging in cells.

    Science.gov (United States)

    Rogers, Nicola J; Claire, Sunil; Harris, Robert M; Farabi, Shiva; Zikeli, Gerald; Styles, Iain B; Hodges, Nikolas J; Pikramenou, Zoe

    2014-01-18

    Gold nanoparticles are efficiently labelled with a luminescent ruthenium complex, producing 13 and 100 nm diameter, monodisperse red-emissive imaging probes with luminescence lifetimes prolonged over the molecular unit. Single, 100 nm particles are observed in whole cell luminescence imaging which reveals their biomolecular association with chromatin in the nucleus of cancer cells.

  10. Measuring the viscous and elastic properties of single cells using video particle tracking microrheology

    CERN Document Server

    Warren, Rebecca Louisa; Li, Xiang; Glidle, Andrew; Carlsson, Allan; Cooper, Jonathan M

    2011-01-01

    We present a simple and \\emph{non-invasive} experimental procedure to measure the linear viscoelastic properties of cells by passive video particle tracking microrheology. In order to do this, a generalised Langevin equation is adopted to relate the time-dependent thermal fluctuations of a bead, chemically bound to the cell's \\emph{exterior}, to the frequency-dependent viscoelastic moduli of the cell. It is shown that these moduli are related to the cell's cytoskeletal structure, which in this work is changed by varying the solution osmolarity from iso- to hypo-osmotic conditions. At high frequencies, the viscoelastic moduli frequency dependence changes from $\\propto \\omega^{3/4}$ found in iso-osmotic solutions to $\\propto \\omega^{1/2}$ in hypo--osmotic solutions; the first situation is typical of bending modes in isotropic \\textit{in vitro} reconstituted F--actin networks, and the second could indicate that the restructured cytoskeleton behaves as a gel with "\\textit{dangling branches}". The insights gained ...

  11. Effect of cyclosporin A particles of varying diameters on gastric cancer cell apoptosis.

    Science.gov (United States)

    Xing, X L; Lu, Y; Qiu, H L

    2016-04-26

    Human health is significantly threatened by gastric cancer, which is the most common malignant tumor; although drastic, surgery is currently the only way to cure it. However, high recurrence rates and low survival rates are associated with the disease. Therefore, to improve the effectiveness of gastric cancer treatment and to increase the clinical cure rate, we investigated the effect of cyclosporin A particles of varying diameter on gastric cancer cell apoptosis. Flow cytometry was used to detect apoptosis induced by Annexin V-fluorescein isothiocyanate/propidium iodide-double labeling. We also determined the content of reactive oxygen species and the expression level of P-glycoprotein in cells after treatment with cyclosporin A. The results indicated that increases in the concentration and action time of cyclosporin A were associated with statistically significant increases in the apoptosis rate of gastric cancer cells when the experimental and control groups were compared (P cyclosporin A inhibits the proliferation of human gastric cancer cells and can induce their apoptosis.

  12. Advanced 3D Poisson solvers and particle-in-cell methods for accelerator modeling

    Energy Technology Data Exchange (ETDEWEB)

    Serafini, David B; McCorquodale, Peter; Colella, Phillip [Lawrence Berkeley National Lab, Applied Numerical Algorithms Group, SciDAC Applied Differential Equations Center (United States)

    2005-01-01

    We seek to improve on the conventional FFT-based algorithms for solving the Poisson equation with infinite-domain (open) boundary conditions for large problems in accelerator modeling and related areas. In particular, improvements in both accuracy and performance are possible by combining several technologies: the method of local corrections (MLC); the James algorithm; and adaptive mesh refinement (AMR). The MLC enables the parallelization (by domain decomposition) of problems with large domains and many grid points. This improves on the FFT-based Poisson solvers typically used as it doesn't require the all-to-all communication pattern that parallel 3d FFT algorithms require, which tends to be a performance bottleneck on current (and foreseeable) parallel computers. In initial tests, good scalability up to 1000 processors has been demonstrated for our new MLC solver. An essential component of our approach is a new version of the James algorithm for infinite-domain boundary conditions for the case of three dimensions. By using a simplified version of the fast multipole method in the boundary-to-boundary potential calculation, we improve on the performance of the Hockney algorithm typically used by reducing the number of grid points by a factor of 8, and the CPU costs by a factor of 3. This is particularly important for large problems where computer memory limits are a consideration. The MLC allows for the use of adaptive mesh refinement, which reduces the number of grid points and increases the accuracy in the Poisson solution. This improves on the uniform grid methods typically used in PIC codes, particularly in beam problems where the halo is large. Also, the number of particles per cell can be controlled more closely with adaptivity than with a uniform grid. To use AMR with particles is more complicated than using uniform grids. It affects depositing particles on the non-uniform grid, reassigning particles when the adaptive grid changes and maintaining the

  13. In vitro comet and micronucleus assays do not predict morphological transforming effects of silica particles in Syrian Hamster Embryo cells.

    Science.gov (United States)

    Darne, Christian; Coulais, Catherine; Terzetti, Francine; Fontana, Caroline; Binet, Stéphane; Gaté, Laurent; Guichard, Yves

    2016-01-15

    Crystalline silica particles and asbestos have both been classified as carcinogenic by the International Agency for Research on Cancer (IARC). However, because of the limited data available, amorphous silica was not classifiable. In vitro, the carcinogenic potential of natural crystalline and amorphous silica particles has been revealed by the Syrian Hamster Embryo (SHE) cell transformation assay. On the other hand, the genotoxic potential of those substances has not been investigated in SHE cells. And yet, genotoxicity assays are commonly used for hazard evaluation and they are often used as in vitro assays of reference to predict a possible carcinogenic potential. The main objective of this study was to compare the genotoxic potential and the carcinogenic potential of different crystalline and amorphous silica particles in SHE cells. Three silica samples of different crystallinity were used: natural amorphous silica, partially crystallized silica and quartz silica particles. Their genotoxicity were tested through the in vitro micronucleus assay and the comet assay in SHE, and their carcinogenic potential through the SHE transformation assay. In addition, silica samples were also tested with the same genotoxicity assays in V79 hamster-lung cells, a common in vitro model for particle exposure. Results obtained in the micronucleus and the comet assays show that none of the silica was capable of inducing genotoxic effects in SHE cells and only the amorphous silica induced genotoxic effects in V79 cells. However in the SHE cell transformation assays, the partially crystallized and quartz silica were able to induce morphological cell transformation. Together, these data suggest that, in vitro, the short-term genotoxic assays alone are not sufficient to predict the hazard and the carcinogenic potential of this type of particles; SHE transformation assay appears a more reliable tool for this purpose and should be included in the "in vitro battery assays" for hazard

  14. The method used to culture host cells (Sf9 cells) can affect the qualities of baculovirus budding particles expressing recombinant proteins.

    Science.gov (United States)

    Hattori, Tomomi; Nakanishi, Kohei; Mori, Takaaki; Tomita, Masahiro; Tsumoto, Kanta

    2016-01-01

    Budded virus (BV) particles of baculovirus (Autographa californica nucleopolyhedrovirus, AcNPV) are harvested from the supernatant of liquid culture of Sf9 host cells by ultracentrifugation. Using polyacrylamide gel electrophoresis, Western blot and transmission electron microscopy (TEM) of BV samples fractionated closely by sucrose density gradient centrifugation, we observed that BVs exhibited different qualities depending on whether they had been harvested from the supernatant from a standing (static), shaking (suspension), or standing/shaking (pre-/post-infection) culture of Sf9 cells. The amount of BV protein apparently increased in the order of standing, standing/shaking, and shaking procedure, and the yield of intact particles showed an opposite trend. TEM observation clearly showed that appropriate fractions of the standing and standing/shaking cultures contained more intact BV particles than those from the shaking culture. These results suggest that the qualities of recombinant BV particles may be related to the culture conditions of the host cells.

  15. Behavior of osteoblast-like cells on calcium-deficient hydroxyapatite ceramics composed of particles with different shapes and sizes.

    Science.gov (United States)

    Kamitakahara, Masanobu; Uno, Yuika; Ioku, Koji

    2014-01-01

    In designing the biomaterials, it is important to control their surface morphologies, because they affect the interactions between the materials and cells. We previously reported that porous calcium-deficient hydroxyapatite (HA) ceramics composed of rod-like particles had advantages over sintered porous HA ceramics; however, the effects of the surface morphology of calcium-deficient HA ceramics on cell behavior have remained unclear. Using a hydrothermal process, we successfully prepared porous calcium-deficient HA ceramics with different surface morphologies, composed of plate-like particles of 200-300, 500-800 nm, or 2-3 μm in width and rod-like particles of 1 or 3-5 μm in width, respectively. The effects of these surface morphologies on the behavior of osteoblast-like cells were examined. Although the numbers of cells adhered to the ceramic specimens did not differ significantly among the specimens, the proliferation rates of cells on the ceramics decreased with decreasing particle size. Our results reveal that controlling the surface morphology that is governed by particle shape and size is important for designing porous calcium-deficient HA ceramics.

  16. A Comparitive Assessement of Cytokine Expression in Human-Derived Cell Lines Exposed to Alpha Particles and X-Rays

    Directory of Open Access Journals (Sweden)

    Vinita Chauhan

    2012-01-01

    Full Text Available Alpha- (α- particle radiation exposure has been linked to the development of lung cancer and has been identified as a radiation type likely to be employed in radiological dispersal devices. Currently, there exists a knowledge gap concerning cytokine modulations associated with exposure to α-particles. Bio-plex technology was employed to investigate changes in proinflammatory cytokines in two human-derived cell lines. Cells were irradiated at a dose of 1.5 Gy to either α-particles or X-rays at equivalent dose rates. The two cell lines exhibited a unique pattern of cytokine expression and the response varied with radiation type. Of the 27 cytokines assessed, only vascular endothelin growth factor (VEGF was observed to be modulated in both cell lines solely after α-particle exposure, and the expression of VEGF was shown to be dose responsive. These results suggest that certain proinflammatory cytokines may be involved in the biological effects related to α- particle exposure and the responses are cell type and radiation type specific.

  17. Dose response of micronuclei induced by combination radiation of α-particles and γ-rays in human lymphoblast cells

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Ruiping; He, Mingyuan; Dong, Chen; Xie, Yuexia; Ye, Shuang; Yuan, Dexiao [Institute of Radiation Medicine, Fudan University, No. 2094 Xie-Tu Road, Shanghai 200032 (China); Shao, Chunlin, E-mail: clshao@shmu.edu.cn [Institute of Radiation Medicine, Fudan University, No. 2094 Xie-Tu Road, Shanghai 200032 (China)

    2013-01-15

    Highlights: ► α-Particle induced MN had a biphasic dose–response followed by a bystander model. ► MN dose–response of α- and γ-combination IR was similar to that of α-particle. ► α-Particles followed by γ-rays yielded a synergistic effect on MN induction. ► Low dose γ-rays triggered antagonistic and adaptive responses against α-particle. - Abstract: Combination radiation is a real situation of both nuclear accident exposure and space radiation environment, but its biological dosimetry is still not established. This study investigated the dose–response of micronuclei (MN) induction in lymphocyte by irradiating HMy2.CIR lymphoblast cells with α-particles, γ-rays, and their combinations. Results showed that the dose–response of MN induced by γ-rays was well-fitted with the linear-quadratic model. But for α-particle irradiation, the MN induction had a biphasic phenomenon containing a low dose hypersensitivity characteristic and its dose response could be well-stimulated with a state vector model where radiation-induced bystander effect (RIBE) was involved. For the combination exposure, the dose response of MN was similar to that of α-irradiation. However, the yield of MN was closely related to the sequence of irradiations. When the cells were irradiated with α-particles at first and then γ-rays, a synergistic effect of MN induction was observed. But when the cells were irradiated with γ-rays followed by α-particles, an antagonistic effect of MN was observed in the low dose range although this combination radiation also yielded a synergistic effect at high doses. When the interval between two irradiations was extended to 4 h, a cross-adaptive response against the other irradiation was induced by a low dose of γ-rays but not α-particles.

  18. Engineering particle morphology and assembly for proton conducting fuel cell membrane applications

    Science.gov (United States)

    Liu, Dongxia

    The development of high performance ion conducting membranes is crucial to the commercialization of polymer electrolyte membrane fuel cells (PEMFCs) and solid oxide fuel cells (SOFCs). This thesis work addresses some of the issues for improving the performance of ion conducting membranes in PEMFCs and SOFCs through engineering membrane microstructures. Electric-field directed particle assembly shows promise as a route to control the structure of polymer composite membranes in PEMFCs. The application of electric fields results in the aggregation of proton conducting particles into particle chains spanning the thickness of composite membranes. The field-induced structure provides improved proton conductivity, selectivity for protons over methanol, and mechanical stability compared to membranes processed without electric field. Hydrothermal deposition is developed as a route to grow electrolyte crystals into membranes (material is hydroxyapatite) with aligned proton conductive pathways that significantly enhance proton transport by eliminating grain boundary resistance. By varying deposition parameters such as reactant concentration, reaction time, or adding crystal growth modifiers, dense hydroxyapatite electrolyte membranes with a range of thickness are produced. The microstructurally engineered hydroxyapatite membranes are promising electrolyte candidates for intermediate temperature fuel cells. The microstructural engineering of ceramics by hydrothermal deposition can potentially be applied to create other ion conducting materials with optimized transport properties. To understand how to control the crystal growth habit by adding growth modifiers, growth of unusual calcite rods was investigated in a microemulsion-based synthesis prior to the investigation of hydrothermal deposition of hydroxyapatite membranes. The microemulsions act as crystal growth modifier to mediate crystal nucleation and subsequent growth. The small microemulsion droplets confine nucleation

  19. Novel methods in the Particle-In-Cell accelerator Code-Framework Warp

    Energy Technology Data Exchange (ETDEWEB)

    Vay, J-L [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Grote, D. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Cohen, R. H. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Friedman, A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2012-12-26

    The Particle-In-Cell (PIC) Code-Framework Warp is being developed by the Heavy Ion Fusion Science Virtual National Laboratory (HIFS-VNL) to guide the development of accelerators that can deliver beams suitable for high-energy density experiments and implosion of inertial fusion capsules. It is also applied in various areas outside the Heavy Ion Fusion program to the study and design of existing and next-generation high-energy accelerators, including the study of electron cloud effects and laser wakefield acceleration for example. This study presents an overview of Warp's capabilities, summarizing recent original numerical methods that were developed by the HIFS-VNL (including PIC with adaptive mesh refinement, a large-timestep 'drift-Lorentz' mover for arbitrarily magnetized species, a relativistic Lorentz invariant leapfrog particle pusher, simulations in Lorentz-boosted frames, an electromagnetic solver with tunable numerical dispersion and efficient stride-based digital filtering), with special emphasis on the description of the mesh refinement capability. In addition, selected examples of the applications of the methods to the abovementioned fields are given.

  20. Particle-in-cell simulation of x-ray wakefield acceleration and betatron radiation in nanotubes

    Science.gov (United States)

    Zhang, Xiaomei; Tajima, Toshiki; Farinella, Deano; Shin, Youngmin; Mourou, Gerard; Wheeler, Jonathan; Taborek, Peter; Chen, Pisin; Dollar, Franklin; Shen, Baifei

    2016-10-01

    Though wakefield acceleration in crystal channels has been previously proposed, x-ray wakefield acceleration has only recently become a realistic possibility since the invention of the single-cycled optical laser compression technique. We investigate the acceleration due to a wakefield induced by a coherent, ultrashort x-ray pulse guided by a nanoscale channel inside a solid material. By two-dimensional particle-in-cell computer simulations, we show that an acceleration gradient of TeV /cm is attainable. This is about 3 orders of magnitude stronger than that of the conventional plasma-based wakefield accelerations, which implies the possibility of an extremely compact scheme to attain ultrahigh energies. In addition to particle acceleration, this scheme can also induce the emission of high energy photons at ˜O (10 - 100 ) MeV . Our simulations confirm such high energy photon emissions, which is in contrast with that induced by the optical laser driven wakefield scheme. In addition to this, the significantly improved emittance of the energetic electrons has been discussed.

  1. On the Numerical Dispersion of the Electromagnetic Particle-In-Cell Code: Finite Grid Instability

    Science.gov (United States)

    Meyers, M. D.; Huang, C.-K.; Zeng, Y.; Yi, S.; Albright, B. J.

    2014-10-01

    The widely used Particle-In-Cell (PIC) method in relativistic particle beam and laser plasma modeling is subject to numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We rigorously derive the faithful 3D PIC numerical dispersion relation, and specialize to the Yee FDTD scheme. The manner in which the PIC algorithm updates and samples the fields and distribution function, along with any temporal and spatial phase factors, is accounted for. Numerical solutions to the 1D dispersion relation are obtained for parameters of interest. We investigate how the finite grid instability arises from the interaction of the numerical modes admitted in the system and their aliases. The most significant interaction is due critically to the correct placement of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rates due to these interactions.

  2. On the Numerical Dispersion of Electromagnetic Particle-In-Cell Code : Finite Grid Instability

    Energy Technology Data Exchange (ETDEWEB)

    Meyers, Michael David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of California, Los Angeles, CA (United States) Dept. of Physics and Astronomy; Huang, Chengkun [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Zeng, Yong [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Yi, Sunghwan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Albright, Brian James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-07-15

    The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the electromagnetic PIC algorithm to analyze the origin of these instabilities. We rigorously derive the faithful 3D numerical dispersion of the PIC algorithm, and then specialize to the Yee FDTD scheme. In particular, we account for the manner in which the PIC algorithm updates and samples the fields and distribution function. Temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme are also explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical 1D modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction.

  3. Physics based optimization of Particle-in-Cell simulations on GPUs

    Science.gov (United States)

    Abbott, Stephen; D'Azevedo, Ed

    2016-10-01

    We present progress in improving the performance of the gyrokinetic particle-in-cell (PIC) code XGC-1 on NVIDIA GPUs, as well as enhancements made to portability and developer productivity using OpenACC directives. Increasingly simulation codes are required to use heterogeneous accelerator resources on the most powerful supercomputing systems. PIC methods are well suited to these massively parallel accelerator architectures, as particles can largely be advanced independently within a time-step. Their advance must still, however, reference field data on underlying grid structures, which presents a significant performance bottleneck. Even ported to GPUs using CUDA Fortran, the XGC-1 electron push routine accounts for a significant portion of the code execution time. By applying physical insight to the motion of electrons across the device (and therefore field grids) we have developed techniques that increase performance of this kernel by up to 5X, compared to the original CUDA Fortran implementation. Architecture specific optimizations can be isolated in small `leaf' routines, which allows for a portable OpenACC implementation that performs nearly as well as the optimized CUDA.

  4. Revealing nonergodic dynamics in living cells from a single particle trajectory.

    Science.gov (United States)

    Lanoiselée, Yann; Grebenkov, Denis S

    2016-05-01

    We propose the improved ergodicity and mixing estimators to identify nonergodic dynamics from a single particle trajectory. The estimators are based on the time-averaged characteristic function of the increments and can thus capture additional information on the process as compared to the conventional time-averaged mean-square displacement. The estimators are first investigated and validated for several models of anomalous diffusion, such as ergodic fractional Brownian motion and diffusion on percolating clusters, and nonergodic continuous-time random walks and scaled Brownian motion. The estimators are then applied to two sets of earlier published trajectories of mRNA molecules inside live Escherichia coli cells and of Kv2.1 potassium channels in the plasma membrane. These statistical tests did not reveal nonergodic features in the former set, while some trajectories of the latter set could be classified as nonergodic. Time averages along such trajectories are thus not representative and may be strongly misleading. Since the estimators do not rely on ensemble averages, the nonergodic features can be revealed separately for each trajectory, providing a more flexible and reliable analysis of single-particle tracking experiments in microbiology.

  5. Local 2D Particle-in-cell simulations of the collisionless MRI

    CERN Document Server

    Riquelme, Mario A; Sharma, Prateek; Spitkovsky, Anatoly

    2012-01-01

    The magnetorotational instability (MRI) is a crucial mechanism of angular momentum transport in a variety of astrophysical accretion disks. In systems accreting at well below the Eddington rate, such as the central black hole in the Milky Way (Sgr A*), the rate of Coulomb collisions between particles is very small, making the disk evolve essentially as a collisionless plasma. We present a nonlinear study of the collisionless MRI using first-principles particle-in-cell (PIC) plasma simulations. In this initial study we focus on local two-dimensional (axisymmetric) simulations, deferring more realistic three-dimensional simulations to future work. For simulations with net vertical magnetic flux, the MRI continuously amplifies the magnetic field until the Alfv\\'en velocity, v_A, is comparable to the speed of light, c (independent of the initial value of v_A/c). This is consistent with the lack of saturation of MRI channel modes in analogous axisymmetric MHD simulations. The amplification of the magnetic field by...

  6. Particle-in-cell simulation study of a lower-hybrid shock

    Science.gov (United States)

    Dieckmann, M. E.; Sarri, G.; Doria, D.; Ynnerman, A.; Borghesi, M.

    2016-06-01

    The expansion of a magnetized high-pressure plasma into a low-pressure ambient medium is examined with particle-in-cell simulations. The magnetic field points perpendicular to the plasma's expansion direction and binary collisions between particles are absent. The expanding plasma steepens into a quasi-electrostatic shock that is sustained by the lower-hybrid (LH) wave. The ambipolar electric field points in the expansion direction and it induces together with the background magnetic field a fast E cross B drift of electrons. The drifting electrons modify the background magnetic field, resulting in its pile-up by the LH shock. The magnetic pressure gradient force accelerates the ambient ions ahead of the LH shock, reducing the relative velocity between the ambient plasma and the LH shock to about the phase speed of the shocked LH wave, transforming the LH shock into a nonlinear LH wave. The oscillations of the electrostatic potential have a larger amplitude and wavelength in the magnetized plasma than in an unmagnetized one with otherwise identical conditions. The energy loss to the drifting electrons leads to a noticeable slowdown of the LH shock compared to that in an unmagnetized plasma.

  7. Particle-in-cell simulation study of a lower-hybrid shock

    CERN Document Server

    Dieckmann, Mark Eric; Doria, Domenico; Ynnerman, Anders; Borghesi, Marco

    2016-01-01

    The expansion of a magnetized high-pressure plasma into a low-pressure ambient medium is examined with particle-in-cell (PIC) simulations. The magnetic field points perpendicularly to the plasma's expansion direction and binary collisions between particles are absent. The expanding plasma steepens into a quasi-electrostatic shock that is sustained by the lower-hybrid (LH) wave. The ambipolar electric field points in the expansion direction and it induces together with the background magnetic field a fast E cross B drift of electrons. The drifting electrons modify the background magnetic field, resulting in its pile-up by the LH shock. The magnetic pressure gradient force accelerates the ambient ions ahead of the LH shock, reducing the relative velocity between the ambient plasma and the LH shock to about the phase speed of the shocked LH wave, transforming the LH shock into a nonlinear LH wave. The oscillations of the electrostatic potential have a larger amplitude and wavelength in the magnetized plasma than...

  8. Projective multiscale time-integration for electrostatic particle-in-cell methods

    CERN Document Server

    Cazeaux, Paul

    2016-01-01

    The simulation of problems in kinetic plasma physics are often challenging due to strongly coupled phenomena across multiple scales. In this work, we propose a wavelet-based coarse-grained numerical scheme, based on the framework of Equation-Free Projective Integration, for a kinetic plasma system modeled by the Vlasov-Poisson equations. A kinetic particle-in-cell (PIC) code is used to simulate the meso scale dynamics for short time intervals. This allows the extrapolation over long time-steps of the behavior of a coarse wavelet-based discretization of the system. To validate the approach and the underlying concepts, we perform two 1D1V numerical experiments: nonlinear propagation and steepening of an ion wave, and the expansion of a plasma slab in vacuum. The direct comparisons to resolved PIC simulations show good agreement. We show that the speedup of the projective integration scheme over the full particle scheme scales linearly with the system size, demonstrating efficiency while taking into account full...

  9. Effect of Different Support Morphologies and Pt Particle Sizes in Electrocatalysts for Fuel Cell Applications

    Directory of Open Access Journals (Sweden)

    G. Sevjidsuren

    2010-01-01

    Full Text Available The performance of a low temperature fuel cell is strongly correlated with parameters like the platinum particle size, platinum dispersion on the carbon support, and electronic and protonic conductivity in the catalyst layer as well as its porosity. These parameters can be controlled by a rational choice of the appropriate catalyst synthesis and carbon support. Only recently, particular attention has been given to the support morphology, as it plays an important role for the formation of the electrode structure. Due to their significantly different structure, mesoporous carbon microbeads (MCMBs and multiwalled carbon nanotubes (MWCNTs were used as supports and compared. Pt nanoparticles were decorated on these supports using the polyol method. Their size was varied by different heating times during the synthesis, and XRD, TEM, SEM, CV, and single cell tests used in their detailed characterization. A membrane-electrode assembly prepared with the MCMB did not show any activity in the fuel cell test, although the catalyst's electrochemical activity was almost similar to the MWCNT. This is assumed to be due to the very dense electrode structure formed by this support material, which does not allow for sufficient mass transport.

  10. Virtual modeling of polycrystalline structures of materials using particle packing algorithms and Laguerre cells

    Science.gov (United States)

    Morfa, Carlos Recarey; Farias, Márcio Muniz de; Morales, Irvin Pablo Pérez; Navarra, Eugenio Oñate Ibañez de; Valera, Roberto Roselló

    2017-06-01

    The influence of the microstructural heterogeneities is an important topic in the study of materials. In the context of computational mechanics, it is therefore necessary to generate virtual materials that are statistically equivalent to the microstructure under study, and to connect that geometrical description to the different numerical methods. Herein, the authors present a procedure to model continuous solid polycrystalline materials, such as rocks and metals, preserving their representative statistical grain size distribution. The first phase of the procedure consists of segmenting an image of the material into adjacent polyhedral grains representing the individual crystals. This segmentation allows estimating the grain size distribution, which is used as the input for an advancing front sphere packing algorithm. Finally, Laguerre diagrams are calculated from the obtained sphere packings. The centers of the spheres give the centers of the Laguerre cells, and their radii determine the cells' weights. The cell sizes in the obtained Laguerre diagrams have a distribution similar to that of the grains obtained from the image segmentation. That is why those diagrams are a convenient model of the original crystalline structure. The above-outlined procedure has been used to model real polycrystalline metallic materials. The main difference with previously existing methods lies in the use of a better particle packing algorithm.

  11. Particle image velocimetry (PIV) study of rotating cylindrical filters for animal cell perfusion processes.

    Science.gov (United States)

    Figueredo-Cardero, Alvio; Chico, Ernesto; Castilho, Leda; de Andrade Medronho, Ricardo

    2012-01-01

    In the present work, the main fluid flow features inside a rotating cylindrical filtration (RCF) system used as external cell retention device for animal cell perfusion processes were investigated using particle image velocimetry (PIV). The motivation behind this work was to provide experimental fluid dynamic data for such turbulent flow using a high-permeability filter, given the lack of information about this system in the literature. The results shown herein gave evidence that, at the boundary between the filter mesh and the fluid, a slip velocity condition in the tangential direction does exist, which had not been reported in the literature so far. In the RCF system tested, this accounted for a fluid velocity 10% lower than that of the filter tip, which could be important for the cake formation kinetics during filtration. Evidence confirming the existence of Taylor vortices under conditions of turbulent flow and high permeability, typical of animal cell perfusion RCF systems, was obtained. Second-order turbulence statistics were successfully calculated. The radial behavior of the second-order turbulent moments revealed that turbulence in this system is highly anisotropic, which is relevant for performing numerical simulations of this system.

  12. Segmentation and abnormality detection of cervical cancer cells using fast elm with particle swarm optimization

    Directory of Open Access Journals (Sweden)

    Sukumar P.

    2015-01-01

    Full Text Available Cervical cancer arises when the anomalous cells on the cervix mature unmanageable obviously in the renovation sector. The most probably used methods to detect abnormal cervical cells are the routine and there is no difference between the abnormal and normal nuclei. So that the abnormal nuclei found are brown in color while normal nuclei are blue in color. The spread or cells are examined and the image denoising is performed based on the Iterative Decision Based Algorithm. Image Segmentation is the method of paneling a digital image into compound sections. The major utilize of segmentation is to abridge or modify the demonstration of an image. The images are segmented by applying anisotropic diffusion on the Denoised image. Image can be enhanced using dark stretching to increase the quality of the image. It separates the cells into all nuclei region and abnormal nuclei region. The abnormal nuclei regions are further classified into touching and non-touching regions and touching regions undergoes feature selection process. The existing Support Vector Machines (SVM is classified few nuclei regions but the time to taken for execution is high. The abnormality detected from the image is calculated as 45% from the total abnormal nuclei. Thus the proposed method of Fast Particle Swarm Optimization with Extreme Learning Machines (Fast PSO-ELM to classify all nuclei regions further into touching region and separated region. The iterative method for to training the ELM and make it more efficient than the SVM method. In experimental result, the proposed method of Fast PSO-ELM may shows the accuracy as above 90% and execution time is calculated based on the abnormality (ratio of abnormal nuclei regions to all nuclei regions image. Therefore, Fast PSO-ELM helps to detect the cervical cancer cells with maximum accuracy.

  13. Low density of membrane particles in auditory hair cells of lizards and birds suggests an absence of somatic motility.

    Science.gov (United States)

    Köppl, Christine; Forge, Andrew; Manley, Geoffrey A

    2004-11-08

    Hair cells are the mechanoreceptive cells of the vertebrate lateral line and inner ear. In addition to their sensory function, hair cells display motility and thus themselves generate mechanical energy, which is thought to enhance sensitivity. Two principal cellular mechanism are known that can mediate hair-cell motility in vitro. One of these is based on voltage-dependent changes of an intramembrane protein and has so far been demonstrated only in outer hair cells of the mammalian cochlea. Correlated with this, the cell membranes of outer hair cells carry an extreme density of embedded particles, as revealed by freeze fracturing. The present study explored the possibility of membrane-based motility in hair cells of nonmammals, by determining their density of intramembrane particles. Replicas of freeze-fractured membrane were prepared from auditory hair cells of a lizard, the Tokay gecko, and a bird, the barn owl. These species were chosen because of independent evidence for active cochlear mechanics, in the form of spontaneous otoacoustic emissions. For quantitative comparison, mammalian inner and outer hair cells, as well as vestibular hair, cells were reevaluated. Lizard and bird hair cells displayed median densities of 2,360 and 1,880 intramembrane particles/microm2, respectively. This was not significantly different from the densities in vestibular and mammalian inner hair cells; however, it was about half the density in of mammalian outer hair cells. This suggests that nonmammalian hair cells do not possess high densities of motor protein in their membranes and are thus unlikely to be capable of somatic motility. 2004 Wiley-Liss, Inc.

  14. Particle-in-cell modeling of streamer branching in CO2 gas

    KAUST Repository

    Levko, Dmitry

    2017-07-07

    The mechanism of streamer branching remains one of the unsolved problems of low-temperature plasma physics. The understanding of this phenomenon requires very high-fidelity models that include, for instance, the kinetic description of electrons. In this paper, we use a two-dimensional particle-in-cell Monte Carlo collisional model to study the branching of anode-directed streamers propagating through short cathode-anode gap filled with atmospheric-pressure CO2 gas. We observe three key phenomena leading to the streamer branching at the considered conditions: flattening of the streamer head, the decrease of the streamer head thickness, and the generation at the streamer head of electrons having the energy larger than 50 eV. For the conditions of our studies, the non-homogeneous distribution of such energetic electrons at the streamer head is probably the primary mechanism responsible for the streamer branching.

  15. WHISTLER TURBULENCE FORWARD CASCADE VERSUS INVERSE CASCADE: THREE-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Ouliang [Oracle Corporation, Redwood Shores, CA (United States); Gary, S. Peter [Space Science Institute, Boulder, CO (United States); Wang, Joseph, E-mail: ouliang@usc.edu, E-mail: pgary@lanl.gov, E-mail: josephjw@usc.edu [University of Southern California, Los Angeles, CA (United States)

    2015-02-20

    We present the results of the first fully three-dimensional particle-in-cell simulations of decaying whistler turbulence in a magnetized, homogeneous, collisionless plasma in which both forward cascades to shorter wavelengths, and inverse cascades to longer wavelengths are allowed to proceed. For the electron beta β {sub e} = 0.10 initial value considered here, the early-time rate of inverse cascade is very much smaller than the rate of forward cascade, so that at late times the fluctuation energy in the regime of the inverse cascade is much weaker than that in the forward cascade regime. Similarly, the wavevector anisotropy in the inverse cascade regime is much weaker than that in the forward cascade regime.

  16. Cis- and cell-type-dependent trans-requirements for Lassa virus-like particle production.

    Science.gov (United States)

    Urata, Shuzo; Yasuda, Jiro

    2015-07-01

    Lassa virus (LASV) small zinc-finger protein (Z), which contains two L-domain motifs, plays a central role in virus budding. Here, we report that co-expression of glycoprotein (GPC) altered the requirements for cholesterol but not the L-domains and host factor, Tsg101, for Z-induced virus-like particle (VLP) production. In particular, the cholesterol requirement for VLP production was cell-type-dependent. In addition, GPC was found to be important for co-localization of Z with CD63, a late endosomal marker. We also found that the N-terminal region (aa 3-10) of Z was critical for its myristoylation and VLP production. These findings will contribute to our understanding of LASV assembly and budding.

  17. A particle-in-cell approach to obliquely propagating electrostatic waves

    Energy Technology Data Exchange (ETDEWEB)

    Koen, Etienne J. [Space Commercial Services Holdings (SCSH) Group, Somerset West (South Africa); School of Electrical Engineering, Royal Institute of Technology (KTH), Stockholm (Sweden); South African National Space Agency (SANSA), Space Science, Hermanus (South Africa); Collier, Andrew B. [University of KwaZulu-Natal, Durban (South Africa); Exegetic Analytics, Durban (South Africa); Maharaj, Shimul K. [South African National Space Agency (SANSA), Space Science, Hermanus (South Africa)

    2014-09-15

    The electron-acoustic and beam-driven modes associated with electron beams have previously been identified and studied numerically. These modes are associated with Broadband Electrostatic Noise found in the Earth's auroral and polar cusp regions. Using a 1-D spatial Particle-in-Cell simulation, the electron-acoustic instability is studied for a magnetized plasma, which includes cool ions, cool electrons and a hot, drifting electron beam. Both the weakly and strongly magnetized regimes with varying wave propagation angle, θ, with respect to the magnetic field are studied. The amplitude and frequency of the electron-acoustic mode are found to decrease with increasing θ. The amplitude of the electron-acoustic mode is found to significantly grow at intermediate wavenumber ranges. It reaches a saturation level at the point, where a plateau forms in the hot electron velocity distribution after which the amplitude of the electron-acoustic mode decays.

  18. Accurate modeling of plasma acceleration with arbitrary order pseudo-spectral particle-in-cell methods

    Science.gov (United States)

    Jalas, S.; Dornmair, I.; Lehe, R.; Vincenti, H.; Vay, J.-L.; Kirchen, M.; Maier, A. R.

    2017-03-01

    Particle in Cell (PIC) simulations are a widely used tool for the investigation of both laser- and beam-driven plasma acceleration. It is a known issue that the beam quality can be artificially degraded by numerical Cherenkov radiation (NCR) resulting primarily from an incorrectly modeled dispersion relation. Pseudo-spectral solvers featuring infinite order stencils can strongly reduce NCR—or even suppress it—and are therefore well suited to correctly model the beam properties. For efficient parallelization of the PIC algorithm, however, localized solvers are inevitable. Arbitrary order pseudo-spectral methods provide this needed locality. Yet, these methods can again be prone to NCR. Here, we show that acceptably low solver orders are sufficient to correctly model the physics of interest, while allowing for parallel computation by domain decomposition.

  19. Accurate modeling of plasma acceleration with arbitrary order pseudo-spectral particle-in-cell methods

    CERN Document Server

    Jalas, Sören; Lehe, Rémi; Vincenti, Henri; Vay, Jean-Luc; Kirchen, Manuel; Maier, Andreas R

    2016-01-01

    Particle in Cell (PIC) simulations are a widely used tool for the investigation of both laser- and beam-driven plasma acceleration. It is a known issue that the beam quality can be artificially degraded by numerical Cherenkov radiation (NCR) resulting primarily from an incorrectly modeled dispersion relation. Pseudo-spectral solvers featuring infinite order stencils can strongly reduce NCR -- or even suppress it -- and are therefore well suited to correctly model the beam properties. For efficient parallelization of the PIC algorithm, however, localized solvers are inevitable. Arbitrary order pseudo-spectral methods provide this needed locality. Yet, these methods can again be prone to NCR. Here, we show that acceptably low solver orders are sufficient to correctly model the physics of interest, while allowing for efficient parallelization.

  20. Linear gyrokinetic particle-in-cell simulations of Alfven instabilities in tokamaks

    CERN Document Server

    Biancalani, A; Briguglio, S; Koenies, A; Lauber, Ph; Mishchenko, A; Poli, E; Scott, B D; Zonca, F

    2015-01-01

    The linear dynamics of Alfven modes in tokamaks is investigated here by means of the global gyrokinetic particle-in-cell code NEMORB. The model equations are shown and the local shear Alfven wave dispersion relation is derived, recovering the continuous spectrum in the incompressible ideal MHD limit. A verification and benchmark analysis is performed for continuum modes in a cylinder and for toroidicity-induced Alfven Eigenmodes. Modes in a reversed-shear equilibrium are also investigated, and the dependence of the spatial structure in the poloidal plane on the equilibrium parameters is described. In particular, a phase-shift in the poloidal angle is found to be present for modes whose frequency touches the continuum, whereas a radial symmetry is found to be characteristic of modes in the continuum gap.

  1. Particle-in-cell modeling of streamer branching in CO2 gas

    Science.gov (United States)

    Levko, Dmitry; Pachuilo, Michael; Raja, Laxminarayan L.

    2017-09-01

    The mechanism of streamer branching remains one of the unsolved problems of low-temperature plasma physics. The understanding of this phenomenon requires very high-fidelity models that include, for instance, the kinetic description of electrons. In this paper, we use a 2D particle-in-cell Monte Carlo collisional model to study the branching of anode-directed streamers propagating through short cathode-anode gap filled with atmospheric-pressure CO2 gas. We observe three key phenomena leading to the streamer branching at the considered conditions: flattening of the streamer head, the decrease of the streamer head thickness, and the generation at the streamer head of electrons having the energy larger than 50 eV. For the conditions of our studies, the non-homogeneous distribution of such energetic electrons at the streamer head is probably the primary mechanism responsible for the streamer branching.

  2. Particle-in-cell investigation on the resonant absorption of a plasma surface wave

    Institute of Scientific and Technical Information of China (English)

    Lan Chao-Hui; Hu Xi-Wei

    2011-01-01

    The resonant absorption of a plasma surface wave is supposed to be an important and efficient mechanism of power deposition for a surface wave plasma source.In this paper,by using the particle-in-cell method and Monte Carlo simulation,the resonance absorption mechanism is investigated.Simulation results demonstrate the existence of surface wave resonance and show the high efficiency of heating electrons.The positions of resonant points,the resonance width and the spatio-temporal evolution of the resonant electric field are presented,which accord well with the theoretical results.The paper also discusses the effect of pressure on the resonance electric field and the plasma density.

  3. Comparing Particle-in-Cell QED Models for High-Intensity Laser-Plasma Interactions

    Science.gov (United States)

    Luedtke, Scott V.; Labun, Lance A.; Hegelich, Björn Manuel

    2016-10-01

    High-intensity lasers, such as the Texas Petawatt, are pushing into new regimes of laser-matter interaction, requiring continuing improvement and inclusion of new physics effects in computer simulations. Experiments at the Texas Petawatt are reaching intensity regimes where new physics-quantum electrodynamics (QED) corrections to otherwise classical plasma dynamics-becomes important. We have two particle-in-cell (PIC) codes with different QED implementations. We review the theory of photon emission in QED-strong fields, and cover the differing PIC implementations. We show predictions from the two codes and compare with ongoing experiments. This work was supported by NNSA cooperative agreement DE-NA0002008, the Defense Advanced Research Projects Agency's PULSE program (12-63-PULSE-FP014) and the Air Force Office of Scientific Research (FA9550-14-1-0045). HPC resources provided by TACC.

  4. Estimation of direct laser acceleration in laser wakefield accelerators using particle-in-cell simulations

    CERN Document Server

    Shaw, J L; Marsh, K A; Tsung, F S; Mori, W B; Joshi, C

    2015-01-01

    Many current laser wakefield acceleration (LWFA) experiments are carried out in a regime where the laser pulse length is on the order of or longer than the wake wavelength and where ionization injection is employed to inject electrons into the wake. In these experiments, the trapped electrons will co-propagate with the longitudinal wakefield and the transverse laser field. In this scenario, the electrons can gain a significant amount of energy from both the direct laser acceleration (DLA) mechanism as well as the usual LWFA mechanism. Particle-in-cell (PIC) codes are frequently used to discern the relative contribution of these two mechanisms. However, if the longitudinal resolution used in the PIC simulations is inadequate, it can produce numerical heating that can overestimate the transverse motion, which is important in determining the energy gain due to DLA. We have therefore carried out a systematic study of this LWFA regime by varying the longitudinal resolution of PIC simulations from the standard, bes...

  5. Two dimensional numerical simulation of gas discharges: comparison between particle-in-cell and FCT techniques

    Energy Technology Data Exchange (ETDEWEB)

    Soria-Hoyo, C; Castellanos, A [Departamento de Electronica y Electromagnetismo, Facultad de Fisica, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla (Spain); Pontiga, F [Departamento de Fisica Aplicada II, EUAT, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla (Spain)], E-mail: cshoyo@us.es

    2008-10-21

    Two different numerical techniques have been applied to the numerical integration of equations modelling gas discharges: a finite-difference flux corrected transport (FD-FCT) technique and a particle-in-cell (PIC) technique. The PIC technique here implemented has been specifically designed for the simulation of 2D electrical discharges using cylindrical coordinates. The development and propagation of a streamer between two parallel electrodes has been used as a convenient test to compare the performance of both techniques. In particular, the phase velocity of the cathode directed streamer has been used to check the internal consistency of the numerical simulations. The results obtained from the two techniques are in reasonable agreement with each other, and both techniques have proved their ability to follow the high gradients of charge density and electric field present in this type of problems. Moreover, the streamer velocities predicted by the simulation are in accordance with the typical experimental values.

  6. Particle-in-cell simulation of Trichel pulses in pure oxygen

    Energy Technology Data Exchange (ETDEWEB)

    Soria-Hoyo, C [Dpto. Electronica y Electromagnetismo, Universidad de Sevilla, Avda. Reina Mercedes s/n, Sevilla 41012 (Spain); Pontiga, F [Dpto. Fisica Aplicada II, Universidad de Sevilla, Avda. Reina Mercedes s/n, Sevilla 41012 (Spain); Castellanos, A [Dpto. Electronica y Electromagnetismo, Universidad de Sevilla, Avda. Reina Mercedes s/n, Sevilla 41012 (Spain)

    2007-08-07

    The development and propagation of Trichel pulses in oxygen have been numerically simulated using an improved fluid particle-in-cell (PIC) method. The numerical method has been optimized to accurately reproduce sequences of about 100 Trichel pulses ({approx}1 ms). A classical one-dimensional model of negative corona in sphere-to-plane geometry has been used to formulate the continuity equations for electrons and ions. The effects of ionization, attachment and secondary-electron emission from the cathode have all been considered. The electric field has been obtained from the solution of Poisson's equation in two dimensions. Using this model, the temporal and electrical characteristics of Trichel pulses have been investigated, in particular, the relation between applied voltage, pulse frequency and time-averaged current intensity and charge.

  7. Electron temperature anisotropy in an expanding plasma: Particle-in-Cell simulations

    CERN Document Server

    Camporeale, Enrico; 10.1088/0004-637X/710/2/1848

    2010-01-01

    We perform fully-kinetic particle-in-cell simulations of an hot plasma that expands radially in a cylindrical geometry. The aim of the paper is to study the consequent development of the electron temperature anisotropy in an expanding plasma flow as found in a collisionless stellar wind. Kinetic plasma theory and simulations have shown that the electron temperature anisotropy is controlled by fluctuations driven by electromagnetic kinetic instabilities. In this study the temperature anisotropy is driven self-consistently by the expansion. While the expansion favors an increase of parallel anisotropy ($T_\\parallel>T_\\perp$), the onset of the firehose instability will tend to decrease it. We show the results for a supersonic, subsonic, and static expansion flows, and suggest possible applications of the results for the solar wind and other stellar winds.

  8. Solution of Poisson's equation in electrostatic Particle-In-Cell simulations

    Science.gov (United States)

    Kahnfeld, Daniel; Schneider, Ralf; Matyash, Konstantin; Lüskow, Karl; Bandelow, Gunnar; Kalentev, Oleksandr; Duras, Julia; Kemnitz, Stefan

    2016-10-01

    For spacecrafts the concept of ion thrusters presents a very efficient method of propulsion. Optimization of thrusters is imperative, but experimental access is difficult. Plasma simulations offer means to understand the plasma physics within an ion thruster and can aid the design of new thruster concepts. In order to achieve best simulation performances, code optimizations and parallelization strategies need to be investigated. In this work the role of different solution strategies for Poisson's equation in electrostatic Particle-in-Cell simulations of the HEMP-DM3a ion thruster was studied. The direct solution method of LU decomposition is compared to a stationary iterative method, the successive over-relaxation solver. Results and runtime of solvers were compared, and an outlook on further improvements and developments is presented. This work was supported by the German Space Agency DLR through Project 50RS1510..

  9. Load management strategy for Particle-In-Cell simulations in high energy physics

    CERN Document Server

    Beck, Arnaud; Derouillat, Julien

    2015-01-01

    In the wake of the intense effort made for the experimental CILEX project, numerical simulation campaigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. By comparing the results given by different codes, it is possible to point out algorithmic limitations both in terms of physical accuracy and computational performances. In this paper we illustrate some of these limitations in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-performance PIC code for high energy physics.

  10. A Particle-in-cell scheme of the RFQ in the SSC-Linac

    Science.gov (United States)

    Xiao, Chen; He, Yuan; Lu, Yuan-Rong; Yuri, Batygin; Yin, Ling; Wang, Zhi-Jun; Yuan, You-Jin; Liu, Yong; Chang, Wei; Du, Xiao-Nan; Wang, Zhi; Xia, Jia-Wen

    2010-11-01

    A 52 MHz Radio Frequency Quadrupole (RFQ) linear accelerator (linac) is designed to serve as an initial structure for the SSC-Linac system (injector into Separated Sector Cyclotron). The designed injection and output energy are 3.5 keV/u and 143 keV/u, respectively. The beam dynamics in this RFQ have been studied using a three-dimensional Particle-In-Cell (PIC) code BEAMPATH. Simulation results show that this RFQ structure is characterized by stable values of beam transmission efficiency (at least 95%) for both zero-current mode and the space charge dominated regime. The beam accelerated in the RFQ has good quality in both transverse and longitudinal directions, and could easily be accepted by Drift Tube Linac (DTL). The effect of the vane error and that of the space charge on the beam parameters have been studied as well to define the engineering tolerance for RFQ vane machining and alignment.

  11. Hamiltonian particle-in-cell methods for Vlasov-Maxwell equations

    Science.gov (United States)

    He, Yang; Sun, Yajuan; Qin, Hong; Liu, Jian

    2016-09-01

    In this paper, we study the Vlasov-Maxwell equations based on the Morrison-Marsden-Weinstein bracket. We develop Hamiltonian particle-in-cell methods for this system by employing finite element methods in space and splitting methods in time. In order to derive the semi-discrete system that possesses a discrete non-canonical Poisson structure, we present a criterion for choosing the appropriate finite element spaces. It is confirmed that some conforming elements, e.g., Nédélec's mixed elements, satisfy this requirement. When the Hamiltonian splitting method is used to discretize this semi-discrete system in time, the resulting algorithm is explicit and preserves the discrete Poisson structure. The structure-preserving nature of the algorithm ensures accuracy and fidelity of the numerical simulations over long time.

  12. Beam Dynamics in an Electron Lens with the Warp Particle-in-cell Code

    CERN Document Server

    Stancari, Giulio; Redaelli, Stefano

    2014-01-01

    Electron lenses are a mature technique for beam manipulation in colliders and storage rings. In an electron lens, a pulsed, magnetically confined electron beam with a given current-density profile interacts with the circulating beam to obtain the desired effect. Electron lenses were used in the Fermilab Tevatron collider for beam-beam compensation, for abort-gap clearing, and for halo scraping. They will be used in RHIC at BNL for head-on beam-beam compensation, and their application to the Large Hadron Collider for halo control is under development. At Fermilab, electron lenses will be implemented as lattice elements for nonlinear integrable optics. The design of electron lenses requires tools to calculate the kicks and wakefields experienced by the circulating beam. We use the Warp particle-in-cell code to study generation, transport, and evolution of the electron beam. For the first time, a fully 3-dimensional code is used for this purpose.

  13. Particle-in-cell simulations of tunneling ionization effects in plasma-based accelerators

    CERN Document Server

    Bruhwiler, D L; Cary, J R; Esarey, E; Leemans, W; Giacone, R E

    2003-01-01

    Plasma-based accelerators can sustain accelerating gradients on the order of 100 GV/m. If the plasma is not fully ionized, fields of this magnitude will ionize neutral atoms via electron tunneling, which can completely change the dynamics of the plasma wake. Particle-in-cell simulations of a high-field plasma wakefield accelerator, using the OOPIC code, which includes field-induced tunneling ionization of neutral Li gas, show that the presence of even moderate neutral gas density significantly degrades the quality of the wakefield. The tunneling ionization model in OOPIC has been validated via a detailed comparison with experimental data from the l'OASIS laboratory. The properties of a wake generated directly from a neutral gas are studied, showing that one can recover the peak fields of the fully ionized plasma simulations, if the density of the electron drive bunch is increased such that the bunch rapidly ionized the gas.

  14. Particle-in-cell Simulations of Global Relativistic Jets with Helical Magnetic Fields

    CERN Document Server

    Duţan, Ioana; Mizuno, Yosuke; Niemiec, Jacek; Kobzar, Oleh; Pohl, Martin; Gómez, Jose L; Pe'er, Asaf; Frederiksen, Jacob T; Nordlund, Åke; Meli, Athina; Sol, Helene; Hardee, Philip E; Hartmann, Dieter H

    2016-01-01

    We study the interaction of relativistic jets with their environment, using 3-dimensional relativistic particle-in-cell simulations for two cases of jet composition: (i) electron-proton ($e^{-}-p^{+}$) and (ii) electron-positron ($e^{\\pm}$) plasmas containing helical magnetic fields. We have performed simulations of "global" jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability and the Mushroom instability. We have found that these kinetic instabilities are suppressed and new types of instabilities can grow. For the $e^{-}-p^{+}$ jet, a recollimation-like instability occurs and jet electrons are strongly perturbed, whereas for the $e^{\\pm}$ jet, a recollimation-like instability occurs at early times followed by kinetic instability and the general structure is similar to a simulation without a helical magnetic field. We plan to perform further simulations using much larger sys...

  15. Parametric decay of a parallel propagating monochromatic whistler wave: Particle-in-cell simulations

    Science.gov (United States)

    Ke, Yangguang; Gao, Xinliang; Lu, Quanming; Wang, Shui

    2017-01-01

    In this paper, by using one-dimensional (1-D) particle-in-cell simulations, we investigate the parametric decay of a parallel propagating monochromatic whistler wave with various wave frequencies and amplitudes. The pump whistler wave can decay into a backscattered daughter whistler wave and an ion acoustic wave, and the decay instability grows more rapidly with the increase of the frequency or amplitude. When the frequency or amplitude is sufficiently large, a multiple decay process may occur, where the daughter whistler wave undergoes a secondary decay into an ion acoustic wave and a forward propagating whistler wave. We also find that during the parametric decay a considerable part of protons can be accelerated along the background magnetic field by the enhanced ion acoustic wave through the Landau resonance. The implication of the parametric decay to the evolution of whistler waves in Earth's magnetosphere is also discussed in the paper.

  16. Particle-In-Cell Modeling of Plasma-Based Accelerators in Two and Three Dimensions

    CERN Document Server

    Hemker, Roy G

    2015-01-01

    In this dissertation, a fully object-oriented, fully relativistic, multi-dimensional Particle-In-Cell code was developed and applied to answer key questions in plasma-based accelerator research. The simulations increase the understanding of the processes in laser plasma and beam-plasma interaction, allow for comparison with experiments, and motivate the development of theoretical models. The simulations support the idea that the injection of electrons in a plasma wave by using a transversely propagating laser pulse is possible. The beam parameters of the injected electrons found in the simulations compare reasonably with beams produced by conventional methods and therefore laser injection is an interesting concept for future plasma-based accelerators. Simulations of the optical guiding of a laser wakefield driver in a parabolic plasma channel support the idea that electrons can be accelerated over distances much longer than the Rayleigh length in a channel. Simulations of plasma wakefield acceleration in the ...

  17. On Energy and Momentum Conservation in Particle-in-Cell Simulation

    CERN Document Server

    Brackbill, J U

    2015-01-01

    Particle-in-cell (PIC) plasma simulations are a productive and valued tool for the study of nonlinear plasma phenomena, yet there are basic questions about the simulation methods themselves that remain unanswered. Here we study one such question: energy and momentum conservation by PIC. We employ both analysis and simulations of one-dimensional, electrostatic plasmas to understand why PIC simulations are either energy or momentum conserving but not both, what the role of numerical stability is in non-conservation, and how do errors in conservation scale with the numerical parameters. Conserving both momentum and energy make it possible to model problems such as Jeans' -type equilibria. Avoiding numerical instability is useful, but so is being able to identify when its effect on the results may be important. Designing simulations to achieve the best possible accuracy with the least expenditure of effort requires results on the scaling of error with the numerical parameters.. Our results identify the central ro...

  18. Gel electrolytes containing several kinds of particles used in quasi-solid-state dye-sensitized solar cells

    Institute of Scientific and Technical Information of China (English)

    GENG Yi; SUN Xiaodan; CAI Qiang; SHI Yantao; LI Hengde

    2006-01-01

    Composite gel electrolytes containing several kinds of particles used as the quasi-solid-state electrolytes in dye-sensitized solar cells (DSSCs) were reported. Mesoporous particles (MCM-41) with unique structures composed of ordered nanochannels were served as a new kind of gelator for quasi-solid-state electrolytes. MCM-41, hydrophobic fumed silica Aerosil R972 and TiO2 nanopatricles P25 were dispersed into gel electrolytes respectively. The solar energy-to-electricity conversion efficiency of these cells is 4.65%, 6.85% and 5.05% respectively under 30 mW·cm-2 illumination. The preparation methods and the particles sizes exert an influence on the performance of corresponding solar cells. Owing to unique pore structures and high specific BET surface area, mesoporous silica MCM-41 was expected to have the potential to afford conducting nanochannels for redox couple diffusion.

  19. Diesel exhaust particle-induced cell death of human leukemic promyelocytic cells HL-60 and their variant cells HL-NR6.

    Science.gov (United States)

    Matsuo, M; Uenishi, R; Shimada, T; Yamanaka, S; Yabuki, M; Utsumi, K; Sagai, M

    2001-04-01

    The cytotoxicity of diesel exhaust particles (DEPs) toward human leukemic promyelocytic cells HL-60 was examined. DEPs were toxic and cytotoxicity increased in a dose-dependent manner. All cells died with 750 microg/ml DEPs in culture media. Apoptosis occurred in HL-60 cells exposed to DEPs. The cytotoxicity of DEP extracts with organic solvents was much lower than those of DEPs and organic solvent-washed residual DEPs. HL-NR6 cells, an HL-60 variant cell line, having higher superoxide dismutase and catalase activities than HL-60 cells, were more resistant to DEP cytotoxicity. When preincubated with the fluorescent probe diacetoxymethyl 6-carboxy-2',7'-dichlorodihydrofluorescinate diacetate and then exposed to DEPs, HL-60 cells emitted green fluorescence under blue illumination, indicating that reactive oxygen species were generated within the cells. The DEP cytotoxicity correlated inversely with the cellular concentration of reduced glutathione (GSH), which had been attenuated with L-buthionine-(R,S)-sulfoximine, a gamma-glutamylcysteine synthetase inhibitor, and was lowered with ethyl reduced glutathionate, a GSH carrier across biomembranes. Further, DEPs themselves decreased the cellular concentration of GSH in a dose-dependent manner. The alpha-tocopherol model compound 2,2,5,7,8-pentamethylchroman-6-ol decreased DEP cytotoxicity, while alpha-tocopherol had no effect. In addition, quinacrine, an endocytosis inhibitor, decreased DEP cytotoxicity. These results show that DEPs are cytotoxic and suggest that the cytotoxicity results from generation of reactive oxygen species by DEPs which have been incorporated into cells.

  20. Effect of labeling with iron oxide particles or nanodiamonds on the functionality of adipose-derived mesenchymal stem cells.

    Directory of Open Access Journals (Sweden)

    Sinead P Blaber

    Full Text Available Stem cells are increasingly the focus of translational research as well as having emerging roles in human cellular therapy. To support these uses there is a need for improved methods for in vivo cell localization and tracking. In this study, we examined the effects of cell labeling on the in vitro functionality of human adipose-derived mesenchymal stem cells. Our results provide a basis for future in vivo studies investigating implanted cell fate and longevity. In particular, we investigated the effects of two different particles: micron-sized (~0.9 µm fluorescently labeled (Dragon Green superparamagnetic iron oxide particles (M-SPIO particles; and, carboxylated nanodiamonds of ~0.25 µm in size. The effects of labeling on the functionality of adipose-derived MSCs were assessed by in vitro morphology, osteogenic and adipogenic differentiation potential, CD marker expression, cytokine secretion profiling and quantitative proteomics of the intra-cellular proteome. The differentiation and CD marker assays for stem-like functionality were not altered upon label incorporation and no secreted or intra-cellular protein changes indicative of stress or toxicity were detected. These in vitro results indicate that the M-SPIO particles and nanodiamonds investigated in this study are biocompatible with MSCs and therefore would be suitable labels for cell localization and tracking in vivo.

  1. Toxicity of nano- and micro-sized silver particles in human hepatocyte cell line L02

    Energy Technology Data Exchange (ETDEWEB)

    Liu Pengpeng; Guan Rongfa; Jiang Jiaxin; Liu Mingqi; Huang Guangrong; Chen Xiaoting [Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018 (China); Ye Xingqian, E-mail: rfguan@163.com [Department of Food Science and Nutrition, School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310029 (China)

    2011-07-06

    Silver nanoparticles (Ag NPs) previously classified as antimicrobial agents have been widely used in consumers and industrial products, especially food storage material. Ag NPs used as antimicrobial agents may be found in liver. Thus, examination of the ability of Ag NPs to penetrate the liver is warranted. The aim of the study was to determine the optimal viability assay for using with Ag NPs in order to assess their toxicity to liver cells. For toxicity evaluations, cellular morphology, mitochondrial function (3-(4, 5-dimethylazol-2-yl)-2, 5-diphenyl-tetrazolium bromide, MTT assay), membrane leakage of lactate dehydrogenase (lactate dehydrogenase, LDH release assay), Oxidative stress markers (malonaldehyde (MDA), glutathione (GSH) and superoxide dismutase (SOD)), DNA damage (single cell gel eletrophoresis, SCGE assay), and protein damage were assessed under control and exposed conditions (24 h of exposure). The results showed that mitochondrial function decreased significantly in cells exposed to Ag NPs at 25 {mu}g{center_dot}mL{sup -1}. LDH leakage significantly increased in cells exposed to Ag NPs ({>=} 25 {mu}g mL{sup -1}) while micro-sized silver particles tested displayed LDH leakage only at higher doses (100 {mu}g{center_dot}mL{sup -1}). The microscopic studies demonstrated that nanoparticle-exposed cells at higher doses became abnormal in size, displaying cellular shrinkage, and an acquisition of an irregular shape. Due to toxicity of silver, further study conducted with reference to its oxidative stress. The results exhibited significant depletion of GSH level, increase in SOD levels and lead to lipid peroxidation, which suggested that cytotoxicity of Ag NPs in liver cells might be mediated through oxidative stress. The results demonstrates that Ag NPs lead to cellular morphological modifications, LDH leakage, mitochondrial dysfunction, and cause increased generation of ROS, depletion of GSH, lipid peroxidation, oxidative DNA damage and protein damage

  2. Toxicity of nano- and micro-sized silver particles in human hepatocyte cell line L02

    Science.gov (United States)

    Liu, Pengpeng; Guan, Rongfa; Ye, Xingqian; Jiang, Jiaxin; Liu, Mingqi; Huang, Guangrong; Chen, Xiaoting

    2011-07-01

    Silver nanoparticles (Ag NPs) previously classified as antimicrobial agents have been widely used in consumers and industrial products, especially food storage material. Ag NPs used as antimicrobial agents may be found in liver. Thus, examination of the ability of Ag NPs to penetrate the liver is warranted. The aim of the study was to determine the optimal viability assay for using with Ag NPs in order to assess their toxicity to liver cells. For toxicity evaluations, cellular morphology, mitochondrial function (3-(4, 5-dimethylazol-2-yl)-2, 5-diphenyl-tetrazolium bromide, MTT assay), membrane leakage of lactate dehydrogenase (lactate dehydrogenase, LDH release assay), Oxidative stress markers (malonaldehyde (MDA), glutathione (GSH) and superoxide dismutase (SOD)), DNA damage (single cell gel eletrophoresis, SCGE assay), and protein damage were assessed under control and exposed conditions (24 h of exposure). The results showed that mitochondrial function decreased significantly in cells exposed to Ag NPs at 25 μg·mL-1. LDH leakage significantly increased in cells exposed to Ag NPs (>= 25 μg mL-1) while micro-sized silver particles tested displayed LDH leakage only at higher doses (100 μg·mL-1). The microscopic studies demonstrated that nanoparticle-exposed cells at higher doses became abnormal in size, displaying cellular shrinkage, and an acquisition of an irregular shape. Due to toxicity of silver, further study conducted with reference to its oxidative stress. The results exhibited significant depletion of GSH level, increase in SOD levels and lead to lipid peroxidation, which suggested that cytotoxicity of Ag NPs in liver cells might be mediated through oxidative stress. The results demonstrates that Ag NPs lead to cellular morphological modifications, LDH leakage, mitochondrial dysfunction, and cause increased generation of ROS, depletion of GSH, lipid peroxidation, oxidative DNA damage and protein damage. Though the exact mechanism behind Ag NPs

  3. Roles of charged particles and reactive species on cell membrane permeabilization induced by atmospheric-pressure plasma irradiation

    Science.gov (United States)

    Sasaki, Shota; Kanzaki, Makoto; Hokari, Yutaro; Tominami, Kanako; Mokudai, Takayuki; Kanetaka, Hiroyasu; Kaneko, Toshiro

    2016-07-01

    As factors that influence cell membrane permeabilization during direct and indirect atmospheric-pressure plasma irradiation, charged particle influx, superoxide anion radicals (O2 -•), and hydrogen peroxide (H2O2) in plasma-irradiated solution were evaluated. These are the three strong candidate factors and might multiply contribute to cell membrane permeabilization. In particular, a shorter plasma diffusion distance leads to the enhancement of the direct effects such as charged particle influx and further increase cell membrane permeability. In addition, O2 -• dissipates over time (a life span of the order of minutes) in plasma-irradiated water, and the deactivation of a plasma-irradiated solution in term of cell membrane permeabilization occurs in a life span of the same order. These results could promote the understanding of the mechanism of plasma-induced cell membrane permeabilization.

  4. Cell Locating with the Image Analysis System of the CAS-LIBB Single-Particle Microbeam Facility

    Institute of Scientific and Technical Information of China (English)

    Wang Xiaohua; Wang Shaohu; Yu Zengliang

    2005-01-01

    A single-particle microbeam facility has been constructed at the Key Laboratory of Ion Beam Bioengineering (LIBB), Chinese Academy of Sciences (CAS). At the CAS-LIBB microbeam facility, we have developed protocols to place exact numbers of charged particles through nuclear centroids of cells, at defined positions in the cytoplasm relative to the nucleus, and through defined fractions of cells in a population. In this paper, we address the methods for nucleus, cytoplasm and bystander (either a single or an exact number of ions is delivered to a certain percentage of cells in a population to study the bystander effects of radiation) irradiation in detail from the precision of target finding and cell locating in the image analysis system. Moreover, for cells touching slightly in an image, a watershed method is used to separate these touching objects;after that, the number of objects in an image is counted accurately and the irradiation points are located precisely.

  5. An oscillating motion of a red blood cell and a neutrally buoyant particle in Poiseuille flow in a narrow channel

    CERN Document Server

    Shi, Lingling; Pan, Tsorng-Whay; Glowinski, Roland

    2013-01-01

    Two motions of oscillation and vacillating breathing (swing) of a red blood cell have been observed in bounded Poiseuille flows (Phys. Rev. E 85, 16307 (2012)). To understand such motions, we have studied the oscillating motion of a neutrally buoyant rigid particle of the same shape in Poiseuille flow in a narrow channel and obtained that the crucial point is to have the particle interacting with Poiseuille flow with its mass center moving up and down in the channel central region. Since the mass center of the cell migrates toward the channel central region, its oscillating motion of the inclination angle is similar to the aforementioned motion as long as the cell keeps the shape of long body. But as the up-and-down oscillation of the cell mass center damps out, the oscillating motion of the inclination angle also damps out and the cell inclination angle approaches to a fixed angle.

  6. Nanometer-scale sizing accuracy of particle suspensions on an unmodified cell phone using elastic light scattering.

    Directory of Open Access Journals (Sweden)

    Zachary J Smith

    Full Text Available We report on the construction of a Fourier plane imaging system attached to a cell phone. By illuminating particle suspensions with a collimated beam from an inexpensive diode laser, angularly resolved scattering patterns are imaged by the phone's camera. Analyzing these patterns with Mie theory results in predictions of size distributions of the particles in suspension. Despite using consumer grade electronics, we extracted size distributions of sphere suspensions with better than 20 nm accuracy in determining the mean size. We also show results from milk, yeast, and blood cells. Performing these measurements on a portable device presents opportunities for field-testing of food quality, process monitoring, and medical diagnosis.

  7. Production of rotavirus core-like particles in Sf9 cells using recombinase-mediated cassette exchange.

    Science.gov (United States)

    Fernandes, Fabiana; Dias, Mafalda M; Vidigal, João; Sousa, Marcos F Q; Patrone, Marco; Teixeira, Ana P; Alves, Paula M

    2014-02-10

    A flexible Sf9 insect cell line was recently developed leveraging the recombinase-mediated cassette exchange (RMCE) technology, which competes with the popular baculovirus expression vector system (BEVS) in terms of speed to produce new proteins. Herein, the ability of this cell platform to produce complex proteins, such as rotavirus core-like particles, was evaluated. A gene construct coding for a VP2-GFP fusion protein was targeted to a pre-characterized high recombination efficiency locus flanked by flipase (Flp) recognition target sites and, after three weeks in selection, an isogenic cell population was obtained. Despite the lower cell specific productivities with respect to those obtained by baculovirus infection, the titers of VP2-GFP reached in shake flask batch cultures were comparable as a result of higher cell densities. To further improve the VP2-GFP levels from stable expression, analysis of exhausted medium was undertaken to design feeding strategies enabling higher cell densities as well as increased culture duration. The implementation of the best strategy allowed reaching 20 million cells per ml in bioreactor cultures; the integrity of the rotavirus core-like particles could be confirmed by electron microscopy. Overall, we show that this Sf9-Flp cell platform represents a valuable alternative to the BEVS for producing complex recombinant proteins, such as rotavirus core-like particles.

  8. The molecular and cellular response of normal and progressed human bronchial epithelial cells to HZE particles

    Science.gov (United States)

    Story, Michael; Ding, Liang-Hao; Minna, John; Park, Seong-mi; Larsen, Jill

    We have used a model of non-oncogenically immortalized normal human bronchial epithelial cells to determine the response of such cells to particles found outside the protection of the earth’s electromagnetic field. We have identified an enhanced frequency of cellular transformation, as measured by growth in soft agar, for both 56Fe and 28Si (1 GeV/n) that is maximal (4-6 fold) at 0.25 Gy and 0.40 Gy, respectively. At 4 months post-irradiation 38 individual soft agar clones were isolated. These clones were characterized extensively for cellular and molecular changes. Gene expression analysis suggested that these clones had down-regulated several genes associated with anti-oxidant pathways including GLS2, GPX1 and 4, SOD2, PIG3, and NQO1 amongst others. As a result, many of these transformed clones were exposed to high levels of intracellular radical oxygen species (ROS), although there appeared not to be any enhanced mitochondrial ROS. DNA repair pathways associated with ATM/ATR signaling were also upregulated. However, these transformants do not develop into tumors when injected into immune-compromised mice, suggesting that they have not progressed sufficiently to become oncogenic. Therefore we chose 6 soft agar clones for continuous culture for an additional 14 months. Amongst the 6 clones, only one clone showed any significant change in phenotype. Clone 3kt-ff.2a, propagated for 18 months, were 2-fold more radioresistant, had a shortened doubling time and the background rate of transformation more than doubled. Furthermore, the morphology of transformed clones changed. Clones from this culture are being compared to the original clone as well as the parental HBEC3KT and will be injected into immune-compromised mice for oncogenic potential. Oncogenically progressed HBECs, HBEC3KT cells that overexpress a mutant RAS gene and where p53 has been knocked down, designated HBEC3KTR53, responded quite differently to HZE particle exposure. First, these cells are more

  9. Neurophysiology of space travel: energetic solar particles cause cell type-specific plasticity of neurotransmission.

    Science.gov (United States)

    Lee, Sang-Hun; Dudok, Barna; Parihar, Vipan K; Jung, Kwang-Mook; Zöldi, Miklós; Kang, Young-Jin; Maroso, Mattia; Alexander, Allyson L; Nelson, Gregory A; Piomelli, Daniele; Katona, István; Limoli, Charles L; Soltesz, Ivan

    2016-11-30

    In the not too distant future, humankind will embark on one of its greatest adventures, the travel to distant planets. However, deep space travel is associated with an inevitable exposure to radiation fields. Space-relevant doses of protons elicit persistent disruptions in cognition and neuronal structure. However, whether space-relevant irradiation alters neurotransmission is unknown. Within the hippocampus, a brain region crucial for cognition, perisomatic inhibitory control of pyramidal cells (PCs) is supplied by two distinct cell types, the cannabinoid type 1 receptor (CB1)-expressing basket cells (CB1BCs) and parvalbumin (PV)-expressing interneurons (PVINs). Mice subjected to low-dose proton irradiation were analyzed using electrophysiological, biochemical and imaging techniques months after exposure. In irradiated mice, GABA release from CB1BCs onto PCs was dramatically increased. This effect was abolished by CB1 blockade, indicating that irradiation decreased CB1-dependent tonic inhibition of GABA release. These alterations in GABA release were accompanied by decreased levels of the major CB1 ligand 2-arachidonoylglycerol. In contrast, GABA release from PVINs was unchanged, and the excitatory connectivity from PCs to the interneurons also underwent cell type-specific alterations. These results demonstrate that energetic charged particles at space-relevant low doses elicit surprisingly selective long-term plasticity of synaptic microcircuits in the hippocampus. The magnitude and persistent nature of these alterations in synaptic function are consistent with the observed perturbations in cognitive performance after irradiation, while the high specificity of these changes indicates that it may be possible to develop targeted therapeutic interventions to decrease the risk of adverse events during interplanetary travel.

  10. Mesoporous silica particle-PLA-PANI hybrid scaffolds for cell-directed intracellular drug delivery and tissue vascularization

    Science.gov (United States)

    Shokry, Hussein; Vanamo, Ulriika; Wiltschka, Oliver; Niinimäki, Jenni; Lerche, Martina; Levon, Kalle; Linden, Mika; Sahlgren, Cecilia

    2015-08-01

    Instructive materials are expected to revolutionize stem cell based tissue engineering. As many stem cell cues have adverse effects on normal tissue homeostasis, there is a need to develop bioactive scaffolds which offer locally retained and cell-targeted drug delivery for intracellular release in targeted cell populations. Further, the scaffolds need to support vascularization to promote tissue growth and function. We have developed an electrospun PLA-PANI fiber scaffold, and incorporated mesoporous silica nanoparticles within the scaffold matrix to obtain cell-targeted and localized drug delivery. The isotropy of the scaffold can be tuned to find the optimal morphology for a given application and the scaffold is electroactive to support differentiation of contractile tissues. We demonstrate that there is no premature drug release from particles under physiological conditions over a period of one week and that the drug is released upon internalization of particles by cells within the scaffold. The scaffold is biocompatible, supports muscle stem cell differentiation and cell-seeded scaffolds are vascularized in vivo upon transplantation on the chorioallantoic membrane of chicken embryos. The scaffold is a step towards instructive biomaterials for local control of stem cell differentiation, and tissue formation supported by vascularization and without adverse effects on the homeostasis of adjacent tissues due to diffusion of biological cues.Instructive materials are expected to revolutionize stem cell based tissue engineering. As many stem cell cues have adverse effects on normal tissue homeostasis, there is a need to develop bioactive scaffolds which offer locally retained and cell-targeted drug delivery for intracellular release in targeted cell populations. Further, the scaffolds need to support vascularization to promote tissue growth and function. We have developed an electrospun PLA-PANI fiber scaffold, and incorporated mesoporous silica nanoparticles within

  11. Adjusted Particle Size Eliminates the Need of Linkage of Antigen and Adjuvants for Appropriated T Cell Responses in Virus-Like Particle-Based Vaccines

    Science.gov (United States)

    Gomes, Ariane C.; Flace, Anna; Saudan, Philippe; Zabel, Franziska; Cabral-Miranda, Gustavo; Turabi, Aadil El; Manolova, Vania; Bachmann, Martin F.

    2017-01-01

    Since the discovery of the first virus-like particle (VLP) derived from hepatitis B virus in 1980 (1), the field has expanded substantially. Besides successful use of VLPs as safe autologous virus-targeting vaccines, the powerful immunogenicity of VLPs has been also harnessed to generate immune response against heterologous and even self-antigens (2–4). Linking adjuvants to VLPs displaying heterologous antigen ensures simultaneous delivery of all vaccine components to the same antigen-presenting cells. As a consequence, antigen-presenting cells, such as dendritic cells, will process and present the antigen displayed on VLPs while receiving costimulatory signals by the VLP-incorporated adjuvant. Similarly, antigen-specific B cells recognizing the antigen linked to the VLP are simultaneously exposed to the adjuvant. Here, we demonstrate in mice that physical association of antigen, carrier (VLPs), and adjuvant is more critical for B than T cell responses. As a model system, we used the E7 protein from human papilloma virus, which spontaneously forms oligomers with molecular weight ranging from 158 kDa to 10 MDa at an average size of 50 nm. E7 oligomers were either chemically linked or simply mixed with VLPs loaded with DNA rich in non-methylated CG motifs (CpGs), a ligand for toll-like receptor 9. E7-specific IgG responses were strongly enhanced if the antigen was linked to the VLPs. In contrast, both CD4+ and CD8+ T cell responses as well as T cell-mediated protection against tumor growth were comparable for linked and mixed antigen formulations. Therefore, our data show that B cell but not T cell responses require antigen-linkage to the carrier and adjuvant for optimal vaccination outcome. PMID:28321220

  12. Absorption enhancement in thin film a-Si solar cells with double-sided SiO2 particle layers

    Institute of Scientific and Technical Information of China (English)

    陈乐; 王庆康; 沈向前; 陈文; 黄堃; 刘代明

    2015-01-01

    Light absorption enhancement is very important for improving the power conversion efficiency of a thin film a-Si solar cell. In this paper, a thin-film a-Si solar cell model with double-sided SiO2 particle layers is designed, and then the underlying mechanism of absorption enhancement is investigated by finite difference time domain (FDTD) simulation;finally the feasible experimental scheme for preparing the SiO2 particle layer is discussed. It is found that the top and bottom SiO2 particle layers play an important role in anti-reflection and light trapping, respectively. The light absorption of the cell with double-sided SiO2 layers greatly increases in a wavelength range of 300 nm–800 nm, and the ultimate efficiency increases more than 22%compared with that of the flat device. The cell model with double-sided SiO2 particle layers reported here can be used in varieties of thin film solar cells to further improve their performances.

  13. Magnetic separation of encapsulated islet cells labeled with superparamagnetic iron oxide nano particles.

    Science.gov (United States)

    Mettler, Esther; Trenkler, Anja; Feilen, Peter J; Wiegand, Frederik; Fottner, Christian; Ehrhart, Friederike; Zimmermann, Heiko; Hwang, Yong Hwa; Lee, Dong Yun; Fischer, Stefan; Schreiber, Laura M; Weber, Matthias M

    2013-01-01

    Islet cell transplantation is a promising option for the restoration of normal glucose homeostasis in patients with type 1 diabetes. Because graft volume is a crucial issue in islet transplantations for patients with diabetes, we evaluated a new method for increasing functional tissue yield in xenogeneic grafts of encapsulated islets. Islets were labeled with three different superparamagnetic iron oxide nano particles (SPIONs; dextran-coated SPION, siloxane-coated SPION, and heparin-coated SPION). Magnetic separation was performed to separate encapsulated islets from the empty capsules, and cell viability and function were tested. Islets labeled with 1000 μg Fe/ml dextran-coated SPIONs experienced a 69.9% reduction in graft volume, with a 33.2% loss of islet-containing capsules. Islets labeled with 100 μg Fe/ml heparin-coated SPIONs showed a 46.4% reduction in graft volume, with a 4.5% loss of capsules containing islets. No purification could be achieved using siloxane-coated SPIONs due to its toxicity to the primary islets. SPION labeling of islets is useful for transplant purification during islet separation as well as in vivo imaging after transplantation. Furthermore, purification of encapsulated islets can also reduce the volume of the encapsulated islets without impairing their function by removing empty capsules.

  14. Immature monocyte derived dendritic cells gene expression profile in response to Virus-Like Particles stimulation

    Directory of Open Access Journals (Sweden)

    Marincola Francesco M

    2005-12-01

    Full Text Available Abstract We have recently developed a candidate HIV-1 vaccine model based on HIV-1 Pr55gag Virus-Like Particles (HIV-VLPs, produced in a baculovirus expression system and presenting a gp120 molecule from an Ugandan HIV-1 isolate of the clade A (HIV-VLPAs. The HIV-VLPAs induce in Balb/c mice systemic and mucosal neutralizing Antibodies as well as cytotoxic T lymphocytes, by intra-peritoneal as well as intra-nasal administration. Moreover, we have recently shown that the baculovirus-expressed HIV-VLPs induce maturation and activation of monocyte-derived dendritic cells (MDDCs which, in turn, produce Th1- and Th2-specific cytokines and stimulate in vitro a primary and secondary response in autologous CD4+ T cells. In the present manuscript, the effects of the baculovirus-expressed HIV-VLPAs on the genomic transcriptional profile of MDDCs obtained from normal healthy donors have been evaluated. The HIV-VLPA stimulation, compared to both PBS and LPS treatment, modulate the expression of genes involved in the morphological and functional changes characterizing the MDDCs activation and maturation. The results of gene profiling analysis here presented are highly informative on the global pattern of gene expression alteration underlying the activation of MDDCs by HIV-VLPAs at the early stages of the immune response and may be extremely helpful for the identification of exclusive activation markers.

  15. Changes in human Langerhans cells following intradermal injection of influenza virus-like particle vaccines.

    Directory of Open Access Journals (Sweden)

    Marc Pearton

    Full Text Available There is a significant gap in our fundamental understanding of early morphological and migratory changes in human Langerhans cells (LCs in response to vaccine stimulation. As the vast majority of LCs studies are conducted in small animal models, substantial interspecies variation in skin architecture and immunity must be considered when extrapolating the results to humans. This study aims to determine whether excised human skin, maintained viable in organ culture, provides a useful human model for measuring and understanding early immune response to intradermally delivered vaccine candidates. Excised human breast skin was maintained viable in air-liquid-interface organ culture. This model was used for the first time to show morphological changes in human LCs stimulated with influenza virus-like particle (VLP vaccines delivered via intradermal injection. Immunohistochemistry of epidermal sheets and skin sections showed that LCs in VLP treated skin lost their typical dendritic morphology. The cells were more dispersed throughout the epidermis, often in close proximity to the basement membrane, and appeared vertically elongated. Our data provides for increased understanding of the complex morphological, spatial and temporal changes that occur to permit LC migration through the densely packed keratinocytes of the epidermis following exposure to vaccine. Significantly, the data not only supports previous animal data but also provides new and essential evidence of host response to this vaccination strategy in the real human skin environment.

  16. Ghost Cell Suspensions as Blood Analogue Fluid for Macroscopic Particle Image Velocimetry Measurements.

    Science.gov (United States)

    Jansen, Sebastian V; Müller, Indra; Nachtsheim, Max; Schmitz-Rode, Thomas; Steinseifer, Ulrich

    2016-02-01

    Spatially resolved measurement of blood flow is of great interest in the development of artificial blood-carrying devices such as blood pumps, heart valve prostheses, and oxygenators. Particle image velocimetry (PIV) is able to measure instantaneous velocity fields in a plane with high accuracy and is being used more frequently for the development of such devices. However, as this measurement technique is based on optical access, blood flow at physiological hematocrit values is difficult to measure due to its low transparency and multiscattering properties. So far, only very small dimensions (in the range of 400 μm) can be measured using PIV. A suspension of ghost cells (GCs) offers a higher optical transparency than blood while having a similar rheological behavior. In this study, a procedure for the production of GC suspensions containing a very low intracellular hemoglobin concentration is presented. With the help of multiple rounds of controlled cell lysis, the intracellular hemoglobin concentration could be decreased to a point where a standard macroscopic PIV measurement was possible. A velocity profile of a 44% GC suspension in a circular channel with a diameter of 9.5 mm was measured with high spatial resolution. Meanwhile, the rheological behavior was found to be comparable with blood.

  17. LIGHT MICROSCOPY DETECTION OF NANOSCALE PARTICLE INTERNALIZATION BY HUMAN LUNG CELLS

    Science.gov (United States)

    RATIONALE. Ultrafine particulate matter (PM) is reported to be more strongly correlated with adverse health effects relative to larger particle size fractions. These epidemiological findings are supported by toxicological studies suggesting that particle size is inversely associa...

  18. Particle-In-Cell Analysis of an Electric Antenna for the BepiColombo/MMO spacecraft

    Science.gov (United States)

    Miyake, Yohei; Usui, Hideyuki; Kojima, Hirotsugu

    The BepiColombo/MMO spacecraft is planned to provide a first electric field measurement in Mercury's magnetosphere by mounting two types of the electric antennas: WPT and MEFISTO. The sophisticated calibration of such measurements should be performed based on precise knowledge of the antenna characteristics in space plasma. However, it is difficult to know prac-tical antenna characteristics considering the plasma kinetics and spacecraft-plasma interactions by means of theoretical approaches. Furthermore, some modern antenna designing techniques such as a "hockey puck" principle is applied to MEFISTO, which introduces much complexity in its overall configuration. Thus a strong demand arises regarding the establishment of a nu-merical method that can solve the complex configuration and plasma dynamics for evaluating the electric properties of the modern instrument. For the self-consistent antenna analysis, we have developed a particle simulation code named EMSES based on the particle-in-cell technique including a treatment antenna conductive sur-faces. In this paper, we mainly focus on electrostatic (ES) features and photoelectron distri-bution in the vicinity of MEFISTO. Our simulation model includes (1) a photoelectron guard electrode, (2) a bias current provided from the spacecraft body to the sensing element, (3) a floating potential treatment for the spacecraft body, and (4) photoelectron emission from sunlit surfaces of the conductive bodies. Of these, the photoelectron guard electrode is a key technol-ogy for producing an optimal condition of plasma environment around MEFISTO. Specifically, we introduced a pre-amplifier housing called puck located between the conductive boom and the sensor wire. The photoelectron guard is then simulated by forcibly fixing the potential difference between the puck surface and the spacecraft body. For the modeling, we use the Capacity Matrix technique in order to assure the conservation condition of total charge owned by the

  19. Yangxueqingnao particles inhibit rat vascular smooth muscle cell proliferation induced by lysophosphatidic acid

    Institute of Scientific and Technical Information of China (English)

    CAI Wei; XU Yi; CHEN Jun-zhu; HUANG Shu-ru; LU Zhen-ya; WANG Zhan-kun

    2005-01-01

    Objective: To observe the effect of Yangxueqingnao particles on rat vascular smooth muscle cell (VSMC) proliferation induced by lysophosphatidic acid (LPA). Methods: The amount of3H-TdR (3H-thymidine) admixed in cultured rat VSMC was measured and mitogen-activated protein kinase (MAPK) activity and lipid peroxidation end product malondialdehyde (MDA)content of the VSMC were assayed. Results: 1×10-9, 1×10-8, 1×10-7 mol/L LPA in a concentration dependent manner, induced the amount of 3H-TdR admixed, MAP kinase activity, and MDA content of the cultured rat VSMC to increase. However, 5%, 10%,and 15% Yangxueqingnao serum preincubation resulted in a decrease of 23.0%, 42.0%, and 52.0% (P<0.01) respectively in the amount of 3H-TdR admixed, a decline in VSMC MAP kinase activity of 13.9% (P<0.05), 29.6% (P<0.01), and 48.9% (P<0.01)respectively, and also, a decrease in MDA content of VSMC of 19.4%, 24.7%, and 43.2% (P<0.01) respectively, in the 1×10-7mol/L LPA-treated VSMC. Conclusions: LPA activates the proliferation and lipid peroxidation of VSMC in a concentration dependent manner. The LPA-induced VSMC proliferation is related to the activity of MAP kinases, enzymes involved in an intracellular signalling pathway. The results of the present study showed that Yangxueqingnao particles can effectively inhibit LPA-induced VSMC proliferation, MAP kinase activation, and reduce lipid peroxidative lesion.

  20. On the numerical dispersion of electromagnetic particle-in-cell code: Finite grid instability

    Science.gov (United States)

    Meyers, M. D.; Huang, C.-K.; Zeng, Y.; Yi, S. A.; Albright, B. J.

    2015-09-01

    The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the Electromagnetic PIC model. We rigorously derive the faithful 3-D numerical dispersion relation of the PIC model, for a simple, direct current deposition scheme, which does not conserve electric charge exactly. We then specialize to the Yee FDTD scheme. In particular, we clarify the presence of alias modes in an eigenmode analysis of the PIC model, which combines both discrete and continuous variables. The manner in which the PIC model updates and samples the fields and distribution function, together with the temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme, is explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1-D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction, which is then verified by simulation. We demonstrate that our analysis is readily extendable to charge conserving models.

  1. Isolation and characterization of Microbulbifer species 6532A degrading seaweed thalli to single cell detritus particles.

    Science.gov (United States)

    Wakabayashi, Masayuki; Sakatoku, Akihiro; Noda, Fumio; Noda, Minoru; Tanaka, Daisuke; Nakamura, Shogo

    2012-02-01

    To reduce the volume of seaweed wastes and extract polysaccharides, seaweed-degrading bacteria were isolated from drifting macroalgae harvested along the coast of Toyama Bay, Japan. Sixty-four bacterial isolates were capable of degrading "Wakame" (Undaria pinnatifida) thallus fragments into single cell detritus (SCD) particles. Amongst these, strain 6532A was the most active degrader of thallus fragments, and was capable of degrading thallus fragments to SCD particles within a day. Although the sequence similarity of the 16S rRNA gene of strain 6532A was 100% similar to that of Microbulbifer elongatus JAMB-A7, several distinct differences were observed between strains, including motility, morphology, and utilization of D: -arabinose and gelatin. Consequently, strain 6532A was classified as a new Microbulbifer strain, and was designated Microbulbifer sp. 6532A. Strain 6532A was capable of degrading both alginate and cellulose in the culture medium, zymogram analysis of which revealed the presence of multiple alginate lyases and cellulases. To the best of our knowledge, this is the first study to directly demonstrate the existence of these enzymes in Microbulbifer species. Shotgun cloning and sequencing of the alginate lyase gene in 6532A revealed a 1,074-bp open reading frame, which was designated algMsp. The reading frame encoded a PL family seven enzyme composed of 358 amino acids (38,181 Da). With a similarity of 74.2%, the deduced amino acid sequence was most similar to a Saccharophagus enzyme (alg 7C). These findings suggest that algMsp in strain 6532A is a novel alginate lyase gene.

  2. A multi-dimensional, energy- and charge-conserving, nonlinearly implicit, electromagnetic Vlasov-Darwin particle-in-cell algorithm

    CERN Document Server

    Chen, Guangye

    2015-01-01

    For decades, the Vlasov-Darwin model has been recognized to be attractive for particle-in-cell (PIC) kinetic plasma simulations in non-radiative electromagnetic regimes, to avoid radiative noise issues and gain computational efficiency. However, the Darwin model results in an elliptic set of field equations that renders conventional explicit time integration unconditionally unstable. Here, we explore a fully implicit PIC algorithm for the Vlasov-Darwin model in multiple dimensions, which overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. The finite-difference scheme for Darwin field equations and particle equations of motion is space-time-centered, employing particle sub-cycling and orbit-averaging. The algorithm conserves total energy, local charge, canonical-momentum in the ignorable direction, and preserves the Coulomb gauge exactly. An asymptotically well-posed fluid preconditioner allows efficient use of large time steps and cell sizes, which are determined by accuracy consid...

  3. Super-resolution imaging of aquaporin-4 orthogonal arrays of particles in cell membranes.

    Science.gov (United States)

    Rossi, Andrea; Moritz, Tobias J; Ratelade, Julien; Verkman, A S

    2012-09-15

    Aquaporin-4 (AQP4) is a water channel expressed in astrocytes, skeletal muscle and epithelial cells that forms supramolecular aggregates in plasma membranes called orthogonal arrays of particles (OAPs). AQP4 is expressed as a short isoform (M23) that forms large OAPs, and a long isoform (M1) that does not form OAPs by itself but can mingle with M23 to form relatively small OAPs. AQP4 OAPs were imaged with ~20 nm spatial precision by photoactivation localization microscopy (PALM) in cells expressing chimeras of M1- or M23-AQP4 with photoactivatable fluorescent proteins. Native AQP4 was imaged by direct stochastic optical reconstruction microscopy (dSTORM) using a primary anti-AQP4 antibody and fluorescent secondary antibodies. We found that OAP area increased from 1878±747 to 3647±958 nm(2) with decreasing M1:M23 ratio from 1:1 to 1:3, and became elongated. Two-color dSTORM indicated that M1 and M23 co-assemble in OAPs with a M1-enriched periphery surrounding a M23-enriched core. Native AQP4 in astrocytes formed OAPs with an area of 2142±829 nm(2), which increased to 5137±1119 nm(2) with 2-bromopalmitate. PALM of AQP4 OAPs in live cells showed slow diffusion (average ~10(-12) cm(2)/s) and reorganization. OAP area was not altered by anti-AQP4 IgG autoantibodies (NMO-IgG) that cause the neurological disease neuromyelitis optica. Super-resolution imaging allowed elucidation of novel nanoscale structural and dynamic features of OAPs.

  4. Direct activation of human dendritic cells by particle-bound but not soluble MHC class II ligand.

    Directory of Open Access Journals (Sweden)

    Renato B Baleeiro

    Full Text Available Dendritic cells (DCs are key activators of cellular immune responses through their capacity to induce naïve T cells and sustained effector T cell responses. This capacity is a function of their superior efficiency of antigen presentation via MHC class I and class II molecules, and the expression of co-stimulatory cell surface molecules and cytokines. Maturation of DCs is induced by microbial factors via pattern recognition receptors such as Toll-like receptors, pro-inflammatory cytokines or cognate interaction with CD4(+ T cells. Here we show that, unexpectedly, the PanDR helper T cell epitope PADRE, a generic T helper cell antigen presented by a large fraction of HLA-DR alleles, when delivered in particle-bound form induced maturation of human DCs. The DCs that received the particle-bound PADRE displayed all features of fully mature DCs, such as high expression of the co-stimulatory molecules CD80, CD86, CD83, the MHC-II molecule HLA-DR, secretion of high levels of the biologically active IL-12 (IL-12p70 and induction of vigorous proliferation of naïve CD4(+ T cells. Furthermore, the maturation of DCs induced by particle-bound PADRE was shown to involve sphingosine kinase, calcium signaling from internal sources and downstream signaling through the MAP kinase and the p72syk pathways, and finally activation of the transcription factor NF-κB. Based on our findings, we propose that particle-bound PADRE may be used as a DC activator in DC-based vaccines.

  5. Influence of particle size and concentration on the diffuse backscattering of polarized light from tissue phantoms and biological cell suspensions

    Energy Technology Data Exchange (ETDEWEB)

    Hielscher, A.H.; Mourant, J.R.; Bigio, I.J. [Los Alamos National Laboratory, Bioscience and Biotechnology, CST-4, MS E535, Los Alamos, New Mexico 87545 (United States)

    1997-01-01

    We present experimental results that show the spatial variations of the diffuse-backscattered intensity when linearly polarized light is incident upon highly scattering media. Experiments on polystyrene-sphere and Intralipid suspensions demonstrate that the radial and azimuthal variations of the observed pattern depend on the concentration, and anisotropy factor {ital g} of the particles that constitute the scattering medium. Measurements performed on biological-cell suspensions show the potential of this method for cell characterization. {copyright} 1997 Optical Society of America

  6. Modeling of photon and pair production due to quantum electrodynamics effects in particle-in-cell simulation

    CERN Document Server

    Wang, W -M; Gibbon, P; Li, Y -T

    2016-01-01

    We develop the particle-in-cell (PIC) code KLAPS to include the photon generation via the Compton scattering and electron-positron creation via the Breit-Wheeler process due to quantum electrodynamics (QED) effects. We compare two sets of existing formulas for the photon generation and different Monte Carlo algorithms. Then we benchmark the PIC simulation results.

  7. Effect of decellularized adipose tissue particle size and cell density on adipose-derived stem cell proliferation and adipogenic differentiation in composite methacrylated chondroitin sulphate hydrogels.

    Science.gov (United States)

    Brown, Cody F C; Yan, Jing; Han, Tim Tian Y; Marecak, Dale M; Amsden, Brian G; Flynn, Lauren E

    2015-07-30

    An injectable composite scaffold incorporating decellularized adipose tissue (DAT) as a bioactive matrix within a hydrogel phase capable of in situ polymerization would be advantageous for adipose-derived stem cell (ASC) delivery in the filling of small or irregular soft tissue defects. Building on previous work, the current study investigates DAT milling methods and the effects of DAT particle size and cell seeding density on the response of human ASCs encapsulated in photo-cross-linkable methacrylated chondroitin sulphate (MCS)-DAT composite hydrogels. DAT particles were generated by milling lyophilized DAT and the particle size was controlled through the processing conditions with the goal of developing composite scaffolds with a tissue-specific 3D microenvironment tuned to enhance adipogenesis. ASC proliferation and adipogenic differentiation were assessed in vitro in scaffolds incorporating small (average diameter of 38   ±   6 μm) or large (average diameter of 278   ±   3 μm) DAT particles in comparison to MCS controls over a period of up to 21 d. Adipogenic differentiation was enhanced in the composites incorporating the smaller DAT particles and seeded at the higher density of 5   ×   10(5) ASCs/scaffold, as measured by glycerol-3-phosphate dehydrogenase (GPDH) enzyme activity, semi-quantitative analysis of perilipin expression and oil red O staining of intracellular lipid accumulation. Overall, this study demonstrates that decellularized tissue particle size can impact stem cell differentiation through cell-cell and cell-matrix interactions, providing relevant insight towards the rational design of composite biomaterial scaffolds for adipose tissue engineering.

  8. Continuously Phase-Modulated Standing Surface Acoustic Waves for Separation of Particles and Cells in Microfluidic Channels Containing Multiple Pressure Nodes

    CERN Document Server

    Lee, Junseok; Kang, Byungjun; Lee, Hyungsuk

    2016-01-01

    This paper describes continuously phase-modulated standing surface acoustic waves (CPM-SSAW) and its application for particle separation in multiple pressure nodes. A linear change of phase in CPM-SSAW applies a force to particles whose magnitude depends on their size and contrast factors. During continuous phase modulation, we demonstrate that particles with the target dimension are translated in the direction of moving pressure nodes, whereas smaller particles show oscillatory movements. The rate of phase modulation is optimized for separation of target particles from the relationship between mean particle velocity and period of oscillation. The developed technique is applied to separate particles of the target dimension from the particle mixture. Furthermore, we also demonstrate human keratinocyte cells can be separated in the cell and bead mixture. The separation technique is incorporated with a microfluidic channel spanning multiple pressure nodes, which is advantageous over separation in a single pressu...

  9. Continuously phase-modulated standing surface acoustic waves for separation of particles and cells in microfluidic channels containing multiple pressure nodes

    Science.gov (United States)

    Lee, Junseok; Rhyou, Chanryeol; Kang, Byungjun; Lee, Hyungsuk

    2017-04-01

    This paper describes continuously phase-modulated standing surface acoustic waves (CPM-SSAW) and its application for particle separation in multiple pressure nodes. A linear change of phase in CPM-SSAW applies a force to particles whose magnitude depends on their size and contrast factors. During continuous phase modulation, we demonstrate that particles with a target dimension are translated in the direction of moving pressure nodes, whereas smaller particles show oscillatory movements. The rate of phase modulation is optimized for separation of target particles from the relationship between mean particle velocity and period of oscillation. The developed technique is applied to separate particles of a target dimension from the particle mixture. Furthermore, we also demonstrate human keratinocyte cells can be separated in the cell and bead mixture. The separation technique is incorporated with a microfluidic channel spanning multiple pressure nodes, which is advantageous over separation in a single pressure node in terms of throughput.

  10. Electron microscopic studies on the uptake of exogenous marker particles by different cell types in the guinea pig metaphysis.

    Science.gov (United States)

    Thyberg, J

    1975-01-01

    Guinea pig metaphyseal bone was exposed to horse spleen ferritin in vitro and to colloidal thorium dioxide in vivo. The cellular uptake and intracellular accumulation of these marker particles were studied ultrastructurally. In vitro, the ferritin molecules were found to spread evely throughout the tissue. After 1-2 hours ferritin was mainly found in plasma membrane invaginations and in endocytic vesicles of varying size. At 4-6 hours a successive accumulation of the marker in secondary lysosomes could be observed. In addition to ferritin, the lysosomes and the large endocytic vesicles often contained other inclusions. In vivo, the pattern of intracellular accumulation of the marker particles was identical to that in vitro. Moreover, the presence within the cells of similar amounts of thorium dioxide after 1 and 4 days suggested that these indigestible molecules are stored intracellularly for a considerable time. In accordance therewith there were no definite signs of extrusion of labeled bodies or secretion of the exogenous marker by exocytosis. Ferritin and thorium dioxide were taken up by all cell types in the metaphysis. Both in vitro and in vivo perivascular cells type B ingested large amounts of marker particles, whereas chondroclasts, endothelial cells. perivascular cells type A and osteoblasts showed a more restricted endocytizing ability. On the basis of these observations, the functional significance of different cell types in the resorption of the epiphyseal cartilage and the formation of bone is discussed.

  11. Measurement of the Interaction Force between Dust Particles within a Glass Box in a GEC RF Reference Cell

    Science.gov (United States)

    Chen, Mudi; Kong, Jie; Qiao, Ke; Carmona-Reyes, Jorge; Harris, Brandon; Matthews, Lorin; Hyde, Truell

    2013-10-01

    A wide variety of structural states (for example, Coulomb balls, one-dimensional vertically aligned dust particle chains, helical dust structures, etc.) have been observed for dust particles confined within a glass box placed on the lower electrode of a GEC rf reference cell. Both the interparticle interaction force and the confinement force play important roles in the formation of these structures. Unfortunately, since the exact nature of the confinement force produced by the walls of the glass box is yet unclear, it is difficult to differentiate between the effects produced by the interparticle interaction force and the effects created by the confinement force. In this experiment, a free-falling dust particle in the box acts as an in-situ probe, providing information on the structure of the confinement force. It will be shown that the data provided by this mapping procedure allows the interaction force between particles within various dust particle structures to be measured through perturbation of individual particles employing a diode pumped solid state laser (Coherent VERDI).

  12. Comparative analysis of charged particle-induced autosomal mutations in murine cells and tissues

    Science.gov (United States)

    Kronenberg, Amy; Gauny, Stacey; Turker, Mitchell; Dan, Cristian; Kwoh, Ely

    Carcinogenesis requires the accumulation of mutations and most of these mutations of occur on autosomes. This study seeks to determine the effect of the tissue microenvironment on the frequency and types of autosomal mutations in epithelial cells exposed to the types of charged particles in space radiation environments. Epithelial cells are the principal cells at risk for the development of solid cancers in humans. Aprt heterozygous mice from a cross between C57BL/6 and DBA/2 mice (B6D2F1) are used for these studies. The tissue of interest here is the kidney. We evaluated the effects of Fe ion on cytotoxicity, mutant frequency, and mutant spectra in kidney epithelium exposed in vivo. In vitro studies use primary kidney clones from B6D2F1 mice. Animals or cells were exposed to graded doses (0-2 Gy) of 1 GeV/amu Fe ions at the NASA Space Radiation Laboratories at Brookhaven National Laboratory. Animals were given whole body exposure in plexiglas holders. Cells were irradiated in T-75 flasks as monolayers. Cytotoxicity for cells exposed as monolayers were performed immediately post-irradiation. In vitro mutation assays were performed after a 5-6 day expression period post-irradiation, at which time cells were seeded in standard medium supplemented with 2,6 diaminopurine to screen for Aprt mutants. Colony formation was assessed in parallel in standard medium. In contrast, mice were euthanized after 2-4 months post-irradiation (early) or 8-10 months post-irradiation (late) to determine the cytotoxic and mutagenic response to Fe ion irradiation. Once the kidneys were digested, the cytotoxicity and mutation assays were performed using the same methodology employed for cells in vitro. Individual Apr t mutant colonies were collected from separate flasks exposed in vitro to 2 Gy of Fe ions. A similar group of Aprt mutants were collected from separate, un-irradiated flasks Aprt mutant colonies were also collected from individual kidneys for un-irradiated mice and for mice

  13. Particle-In-Cell simulation concerning heat-flux mitigation using electromagnetic fields

    Science.gov (United States)

    Lüskow, Karl Felix; Duras, Julia; Kemnitz, Stefan; Kahnfeld, Daniel; Matthias, Paul; Bandelow, Gunnas; Schneider, Ralf; Konigorski, Detlev

    2016-10-01

    In space missions enormous amount of money is spent for the thermal protection system for re-entry. To avoid complex materials and save money one idea is to reduce the heat-flux towards the spacecraft. The partially-ionized gas can be controlled by electromagnetic fields. For first-principle tests partially ionized argon flow from an arc-jet was used to measure the heat-flux mitigation created by an external magnetic field. In the successful experiment a reduction of 85% was measured. In this work the Particle-in-Cell (PIC) method was used to simulate this experiment. PIC is able to reproduce the heat flux mitigation qualitatively. The main mechanism is identified as a changed electron transport and by this, modified electron density due to the reaction to the applied magnetic field. Ions follow due to quasi-neutrality and influence then strongly by charge exchange collisions the neutrals dynamics and heat deposition. This work was supported by the German Space Agency DLR through Project 50RS1508.

  14. Simulation of a Smith-Purcell FEL Using a Particle-in-Cell Code

    CERN Document Server

    Donohue, J T

    2005-01-01

    A simulation of the generation of Smith-Purcell (S-P) radiation at microwave frequencies is performed using the two-dimensional particle-in-cell code MAGIC. The simulation supposes that a continuous, thin (but infinitely wide), mono-energetic electron beam passes over a diffraction grating, while a strong axial magnetic field constrains the electrons to essentially one-dimensional motion. We find that the passage of the beam excites an evanescent electromagnetic wave in the proximity of the grating, which in turn leads to bunching of the initially continuous electron beam. The frequency and wave number of the bunching are determined, and found to be close to those proposed by Brau and co-workers in recent work [1]. This frequency is below the threshold for S-P radiation. However, the bunching is sufficiently strong that higher harmonics are clearly visible in the beam current. These harmonic frequencies correspond to allowed S-P radiation, and we see strong emission of such radiation at the appropriate angles...

  15. Validation and benchmarking of two particle-in-cell codes for a glow discharge

    Science.gov (United States)

    Carlsson, Johan; Khrabrov, Alexander; Kaganovich, Igor; Sommerer, Timothy; Keating, David

    2017-01-01

    The two particle-in-cell codes EDIPIC and LSP are benchmarked and validated for a parallel-plate glow discharge in helium, in which the axial electric field had been carefully measured, primarily to investigate and improve the fidelity of their collision models. The scattering anisotropy of electron-impact ionization, as well as the value of the secondary-electron emission yield, are not well known in this case. The experimental uncertainty for the emission yield corresponds to a factor of two variation in the cathode current. If the emission yield is tuned to make the cathode current computed by each code match the experiment, the computed electric fields are in excellent agreement with each other, and within about 10% of the experimental value. The non-monotonic variation of the width of the cathode fall with the applied voltage seen in the experiment is reproduced by both codes. The electron temperature in the negative glow is within experimental error bars for both codes, but the density of slow trapped electrons is underestimated. A more detailed code comparison done for several synthetic cases of electron-beam injection into helium gas shows that the codes are in excellent agreement for ionization rate, as well as for elastic and excitation collisions with isotropic scattering pattern. The remaining significant discrepancies between the two codes are due to differences in their electron binary-collision models, and for anisotropic scattering due to elastic and excitation collisions.

  16. Comparison of dust charging between Orbital-Motion-Limited theory and Particle-In-Cell simulations

    CERN Document Server

    Delzanno, Gian Luca

    2016-01-01

    The Orbital-Motion-Limited (OML) theory has been modified to predict the dust charge and the results were contrasted with the Whipple approximation [Tang and Delzanno, Phys. Plasmas 21, 123708 (2014)]. To further establish its regime of applicability, in this paper the OML predictions (for a non-electron-emitting, spherical dust grain at rest in a collisionless, unmagnetized plasma) are compared with Particle-In-Cell simulations that retain the absorption radius effect. It is found that for large dust grain radius $r_d$ relative to the plasma Debye length $\\lambda_D$, the revised OML theory remains a very good approximation as, for the parameters considered ($r_d/\\lambda_D\\le10$, equal electron and ion temperatures), it yields the dust charge to within $20\\%$ accuracy. This is a substantial improvement over the Whipple approximation. The dust collected currents and energy fluxes, which remain the same in the revised and standard OML theories, are accurate to within $15-30\\%$.

  17. MHD-EPIC: Extended Magnetohydrodynamics with Embedded Particle-in-Cell Simulation of Ganymede's Magnetosphere.

    Science.gov (United States)

    Toth, G.; Daldorff, L. K. S.; Jia, X.; Gombosi, T. I.; Lapenta, G.

    2014-12-01

    We have recently developed a new modeling capability to embed theimplicit Particle-in-Cell (PIC) model iPIC3D into the BATS-R-USmagnetohydrodynamic model. The PIC domain can cover the regions wherekinetic effects are most important, such as reconnection sites. TheBATS-R-US code, on the other hand, can efficiently handle the rest ofthe computational domain where the MHD or Hall MHD description issufficient. As one of the very first applications of the MHD-EPICalgorithm (Daldorff et al. 2014, JCP, 268, 236) we simulate theinteraction between Jupiter's magnetospheric plasma with Ganymede'smagnetosphere, where the separation of kinetic and global scalesappears less severe than for the Earth's magnetosphere. Because theexternal Jovian magnetic field remains in an anti-parallel orientationwith respect to Ganymede's intrinsic magnetic field, magneticreconnection is believed to be the major process that couples the twomagnetospheres. As the PIC model is able to describe self-consistentlythe electron behavior, our coupled MHD-EPIC model is well suited forinvestigating the nature of magnetic reconnection in thisreconnection-driven mini-magnetosphere. We will compare the MHD-EPICsimulations with pure Hall MHD simulations and compare both modelresults with Galileo plasma and magnetic field measurements to assess therelative importance of ion and electron kinetics in controlling theconfiguration and dynamics of Ganymede's magnetosphere.

  18. Particle-in-Cell Modeling of Magnetized Argon Plasma Flow Through Small Mechanical Apertures

    Energy Technology Data Exchange (ETDEWEB)

    Adam B. Sefkow and Samuel A. Cohen

    2009-04-09

    Motivated by observations of supersonic argon-ion flow generated by linear helicon-heated plasma devices, a three-dimensional particle-in-cell (PIC) code is used to study whether stationary electrostatic layers form near mechanical apertures intersecting the flow of magnetized plasma. By self-consistently evaluating the temporal evolution of the plasma in the vicinity of the aperture, the PIC simulations characterize the roles of the imposed aperture and applied magnetic field on ion acceleration. The PIC model includes ionization of a background neutral-argon population by thermal and superthermal electrons, the latter found upstream of the aperture. Near the aperture, a transition from a collisional to a collisionless regime occurs. Perturbations of density and potential, with mm wavelengths and consistent with ion acoustic waves, propagate axially. An ion acceleration region of length ~ 200-300 λD,e forms at the location of the aperture and is found to be an electrostatic double layer, with axially-separated regions of net positive and negative charge. Reducing the aperture diameter or increasing its length increases the double layer strength.

  19. Magnetohydrodynamics with Embedded Particle-in-Cell Simulation of Mercury's Magnetosphere

    Science.gov (United States)

    Chen, Y.; Toth, G.; Jia, X.; Gombosi, T. I.; Markidis, S.

    2015-12-01

    Mercury's magnetosphere is much more dynamic than other planetary magnetospheres because of Mercury's weak intrinsic magnetic field and its proximity to the Sun. Magnetic reconnection and Kelvin-Helmholtz phenomena occur in Mercury's magnetopause and magnetotail at higher frequencies than in other planetary magnetosphere. For instance, chains of flux transfer events (FTEs) on the magnetopause, have been frequentlyobserved by the the MErcury Surface, Space ENvironment, GEochemistry and Ranging (MESSENGER) spacecraft (Slavin et al., 2012). Because ion Larmor radius is comparable to typical spatial scales in Mercury's magnetosphere, finite Larmor radius effects need to be accounted for. In addition, it is important to take in account non-ideal dissipation mechanisms to accurately describe magnetic reconnection. A kinetic approach allows us to model these phenomena accurately. However, kinetic global simulations, even for small-size magnetospheres like Mercury's, are currently unfeasible because of the high computational cost. In this work, we carry out global simulations of Mercury's magnetosphere with the recently developed MHD-EPIC model, which is a two-way coupling of the extended magnetohydrodynamic (XMHD) code BATS-R-US with the implicit Particle-in-Cell (PIC) model iPIC3D. The PIC model can cover the regions where kinetic effects are most important, such as reconnection sites. The BATS-R-US code, on the other hand, can efficiently handle the rest of the computational domain where the MHD or Hall MHD description is sufficient. We will present our preliminary results and comparison with MESSENGER observations.

  20. Particle-In-Cell Simulation on the Characteristics of a Receiving Antenna in Space Plasma Environment

    Science.gov (United States)

    Miyake, Yohei; Usui, Hideyuki; Kojima, Hirotsugu; Omura, Yoshiharu

    2008-12-01

    We applied the electromagnetic Particle-In-Cell simulation to the analysis of receiving antenna characteristics in space plasma environment. In the analysis, we set up external waves in a simulation region and receive them with a numerical antenna model placed in the simulation region. Using this method, we evaluated the effective length of electric field antennas used for plasma wave investigations conducted by scientific spacecraft. We particularly focused on the effective length of an electric field instrument called MEFISTO for a future mission to Mercury: BepiColombo. We first confirmed that the effective length of the MEFISTO-type antenna is basically longer than that of a simple dipole antenna for both electrostatic and electromagnetic plasma waves. By applying the principle of a voltmeter, the effective length of the MEFISTO-type antenna is predicted to become identical to the separation between two sensor-conductor's midpoints. However, the numerical result revealed that the actual effective length becomes shorter than the prediction, which is caused by the shorting-out effect due to the presence of a center boom conductor between the two sensor conductors. Since the above effect is difficult to treat theoretically, the present numerical method is a powerful tool for further quantitative evaluation of the antenna characteristics.

  1. Low aspect ratio micropores for single-particle and single-cell analysis.

    Science.gov (United States)

    Goyal, Gaurav; Mulero, Rafael; Ali, Jamel; Darvish, Armin; Kim, Min Jun

    2015-05-01

    This paper describes microparticle and bacterial translocation studies using low aspect ratio solid-state micropores. Micropores, 5 μm in diameter, were fabricated in 200 nm thick free-standing silicon nitride membranes, resulting in pores with an extremely low aspect ratio, nominally 0.04. For microparticle translocation experiments, sulfonated polystyrene microparticles and magnetic microbeads in size range of 1-4 μm were used. Using the microparticle translocation characteristics, we find that particle translocations result in a change only in the pore's geometrical resistance while the access resistance remains constant. Furthermore, we demonstrate the ability of our micropore to probe high-resolution shape information of translocating analytes using concatenated magnetic microspheres. Distinct current drop peaks were observed for each microsphere of the multibead architecture. For bacterial translocation experiments, nonflagellated Escherichia coli (strain HCB 5) and wild type flagellated Salmonella typhimurium (strain SJW1103) were used. Distinct current signatures for the two bacteria were obtained and this difference in translocation behavior was attributed to different surface protein distributions on the bacteria. Our findings may help in developing low aspect ratio pores for high-resolution microparticle characterization and single-cell analysis.

  2. Three-dimensional particle-in-cell simulation on gain saturation effect of microchannel plate.

    Science.gov (United States)

    Wang, Qiangqiang; Yuan, Zheng; Cao, Zhurong; Deng, Bo; Chen, Tao; Deng, Keli

    2016-07-01

    We present here the results of the simulation work, using the three-dimensional particle-in-cell method, on the performance of the lead glass microchannel plate under saturated state. We calculated the electron cascade process with different DC bias voltages under both self-consistent condition and non-self-consistent condition. The comparative results have demonstrated that the strong self-consistent field can suppress the cascade process and make the microchannel plate saturated. The simulation results were also compared to the experimental data and good agreement was obtained. The simulation results also show that the electron multiplication process in the channel is accompanied by the buildup process of positive charges in the channel wall. Though the interactions among the secondary electron cloud in the channel, the positive charges in the channel wall, and the external acceleration field can make the electron-surface collision more frequent, the collision energy will be inevitably reduced, thus the electron gain will also be reduced.

  3. Electron Debye scale Kelvin-Helmholtz instability: Electrostatic particle-in-cell simulations

    Science.gov (United States)

    Lee, Sang-Yun; Lee, Ensang; Kim, Khan-Hyuk; Lee, Dong-Hun; Seon, Jongho; Jin, Ho

    2015-12-01

    In this paper, we investigated the electron Debye scale Kelvin-Helmholtz (KH) instability using two-dimensional electrostatic particle-in-cell simulations. We introduced a velocity shear layer with a thickness comparable to the electron Debye length and examined the generation of the KH instability. The KH instability occurs in a similar manner as observed in the KH instabilities in fluid or ion scales producing surface waves and rolled-up vortices. The strength and growth rate of the electron Debye scale KH instability is affected by the structure of the velocity shear layer. The strength depends on the magnitude of the velocity and the growth rate on the velocity gradient of the shear layer. However, the development of the electron Debye scale KH instability is mainly determined by the electric field generated by charge separation. Significant mixing of electrons occurs across the shear layer, and a fraction of electrons can penetrate deeply into the opposite side fairly far from the vortices across the shear layer.

  4. Particle-in-Cell Simulations of the VENUS Ion Beam Transport System

    CERN Document Server

    Todd, Damon; Leitner, Daniela; Lyneis, Claude; Qiang, Ji

    2005-01-01

    The next-generation superconducting ECR ion source VENUS serves as the prototype injector ion source for the linac driver of the proposed Rare Isotope Accelerator (RIA). The high-intensity heavy ion beams required by the RIA driver linac present significant challenges for the design and simulation of an ECR extraction and low energy ion beam transport system. Extraction and beam formation take place in a strong (up to 3T) axial magnetic field, which leads to significantly different focusing properties for the different ion masses and charge states of the extracted beam. Typically, beam simulations must take into account the contributions of up to 30 different charge states and ion masses. Two three-dimensional, particle-in-cell codes developed for other purposes, IMPACT and WARP, have been adapted in order to model intense, multi-species DC beams. A discussion of the differences of these codes and the advantages of each in the simulation of the low energy beam transport system of an ECR ion source is given. D...

  5. A two-dimensional (azimuthal-axial) particle-in-cell model of a Hall thruster

    Energy Technology Data Exchange (ETDEWEB)

    Coche, P.; Garrigues, L., E-mail: laurent.garrigues@laplace.univ-tlse.fr [LAPLACE (Laboratoire Plasma et Conversion d' Energie), Université de Toulouse, UPS, INPT Toulouse 118, route de Narbonne, F-31062 Toulouse cedex 9 (France); CNRS, LAPLACE, F-31062 Toulouse (France)

    2014-02-15

    We have developed a two-dimensional Particle-In-Cell model in the azimuthal and axial directions of the Hall thruster. A scaling method that consists to work at a lower plasma density to overcome constraints on time-step and grid-spacing is used. Calculations are able to reproduce the breathing mode due to a periodic depletion of neutral atoms without the introduction of a supplementary anomalous mechanism, as in fluid and hybrid models. Results show that during the increase of the discharge current, an electron-cyclotron drift instability (frequency in the range of MHz and wave number on the order of 3000 rad s{sup −1}) is formed in the region of the negative gradient of magnetic field. During the current decrease, an axial electric wave propagates from the channel toward the exhaust (whose frequency is on the order of 400 kHz) leading to a broadening of the ion energy distribution function. A discussion about the influence of the scaling method on the calculation results is also proposed.

  6. On energy and momentum conservation in particle-in-cell plasma simulation

    Science.gov (United States)

    Brackbill, J. U.

    2016-07-01

    Particle-in-cell (PIC) plasma simulations are a productive and valued tool for the study of nonlinear plasma phenomena, yet there are basic questions about the simulation methods themselves that remain unanswered. Here we study energy and momentum conservation by PIC. We employ both analysis and simulations of one-dimensional, electrostatic plasmas to understand why PIC simulations are either energy or momentum conserving but not both, what role a numerical stability plays in non-conservation, and how errors in conservation scale with the numerical parameters. Conserving both momentum and energy make it possible to model problems such as Jeans'-type equilibria. Avoiding numerical instability is useful, but so is being able to identify when its effect on the results may be important. Designing simulations to achieve the best possible accuracy with the least expenditure of effort requires results on the scaling of error with the numerical parameters. Our results identify the central role of Gauss' law in conservation of both momentum and energy, and the significant differences in numerical stability and error scaling between energy-conserving and momentum-conserving simulations.

  7. Kinetic structures of quasi-perpendicular shocks in global particle-in-cell simulations

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ivy Bo, E-mail: bopeng@kth.se; Markidis, Stefano; Laure, Erwin [KTH Royal Institute of Technology, Stockholm (Sweden); Johlander, Andreas; Vaivads, Andris; Khotyaintsev, Yuri [Swedish Institute of Space Physics, Uppsala (Sweden); Henri, Pierre [LPC2E-CNRS, Orléans (France); Lapenta, Giovanni [Centre for mathematical Plasma-Astrophysics, KU Leuven, Leuven (Belgium)

    2015-09-15

    We carried out global Particle-in-Cell simulations of the interaction between the solar wind and a magnetosphere to study the kinetic collisionless physics in super-critical quasi-perpendicular shocks. After an initial simulation transient, a collisionless bow shock forms as a result of the interaction of the solar wind and a planet magnetic dipole. The shock ramp has a thickness of approximately one ion skin depth and is followed by a trailing wave train in the shock downstream. At the downstream edge of the bow shock, whistler waves propagate along the magnetic field lines and the presence of electron cyclotron waves has been identified. A small part of the solar wind ion population is specularly reflected by the shock while a larger part is deflected and heated by the shock. Solar wind ions and electrons are heated in the perpendicular directions. Ions are accelerated in the perpendicular direction in the trailing wave train region. This work is an initial effort to study the electron and ion kinetic effects developed near the bow shock in a realistic magnetic field configuration.

  8. Electrostatic particle-in-cell simulation of heat flux mitigation using magnetic fields

    Science.gov (United States)

    Lüskow, Karl Felix; Kemnitz, S.; Bandelow, G.; Duras, J.; Kahnfeld, D.; Matthias, P.; Schneider, R.; Konigorski, D.

    2016-10-01

    The particle-in-cell (PIC) method was used to simulate heat flux mitigation experiments with partially ionised argon. The experiments demonstrate the possibility of reducing heat flux towards a target using magnetic fields. Modelling using the PIC method is able to reproduce the heat flux mitigation qualitatively. This is driven by modified electron transport. Electrons are magnetised and react directly to the external magnetic field. In addition, an increase of radial turbulent transport is also needed to explain the experimental observations in the model. Close to the target an increase of electron density is created. Due to quasi-neutrality, ions follow the electrons. Charge exchange collisions couple the dynamics of the neutrals to the ions and reduce the flow velocity of neutrals by radial momentum transport and subsequent losses. By this, the dominant heat-transport channel by neutrals gets reduced and a reduction of the heat deposition, similar to the experiment, is observed. Using the simulation a diagnostic module for optical emission is developed and its results are compared with spectroscopic measurements and photos from the experiment. The results of this study are in good agreement with the experiment. Experimental observations such as a shrank bright emission region close to the nozzle exit, an additional emission in front of the target and an overall change in colour to red are reproduced by the simulation.

  9. Kinetic Structures of Quasi-Perpendicular Shocks in Global Particle-in-Cell Simulations

    Science.gov (United States)

    Peng, I. B.; Markidis, S.; Laure, E.; Johlander, A.; Vaivads, A.; Khotyaintsev, Y. V.; Pierre, H.; Lapenta, G.

    2015-12-01

    We carried out global Particle-in-Cell simulations of the interaction between the solar wind and a magnetosphere to study the kinetic collisionless physics in super-critical quasi-perpendicular shocks. After an initial simulation transient, a collisionless bow shock forms as a result of the interaction of the solar wind and a planet magnetic dipole. The shock ramp has a thickness of approximately one ion skin depth and is followed by a trailing wave train in the shock downstream. At the downstream edge of the bow shock, whistler waves propagate along the magnetic field lines and the presence of electron cyclotron waves has been identified. A small part of the solar wind ion population is specularly reflected by the shock while a larger part is deflected and heated by the shock. Solar wind ions and electrons are heated in the perpendicular directions. Ions are accelerated in the perpendicular direction in the trailing wave train region. This work is an initial effort to study the electron and ion kinetic effects developed near the bow shock in a realistic magnetic field configuration.

  10. Particle-in-cell study of the ion-to-electron sheath transition

    CERN Document Server

    Scheiner, Brett; Hopkins, Matthew M; Yee, Benjamin T; Barnat, Edward V

    2016-01-01

    The form of a sheath near a small electrode, with bias changing from below to above the plasma potential is studied using 2D particle-in-cell (PIC) simulations. Five cases are studied: (A) an electrode biased more than the electron temperature ($T_e/e$) below the plasma potential, (B) an electrode biased less than $T_e/2e$ below the plasma potential, (C) an electrode biased nearly at the plasma potential, (D) an electrode biased more than $T_i/2e$ but less than $T_e/2e$ above the plasma potential, and (E) an electrode biased much greater than $T_e/2e$ above the plasma potential. In case (A), the electron velocity distribution function (EVDF) is observed to be Maxwellian with a Boltzmann-type exponential density decay through the ion sheath and presheath. In cases (B) and (C), the EVDFs exhibit a loss-cone type truncation due to fast electrons overcoming the small potential difference between the electrode and plasma. No sheath is present in this regime, and the plasma remains quasineutral up to the electrode....

  11. Gyrokinetic and kinetic particle-in-cell simulations of guide-field reconnection

    Science.gov (United States)

    Munoz Sepulveda, Patricio Alejandro; Büchner, Jörg; Kilian, Patrick; Told, Daniel; Jenko, Frank

    2016-07-01

    Fully kinetic Particle-in-Cell (PIC) simulations of (strong) guide-field reconnection can be computationally very demanding, due to the intrinsic stability and accuracy conditions required by this numerical method. One convenient approach to circumvent this issue is using gyrokinetic theory, an approximation of the Vlasov-Maxwell equations for strongly magnetized plasmas that eliminates the fast gyromotion, and thus reduces the computational cost. Although previous works have started to compare the features of reconnection between both approaches, a complete understanding of the differences is far from being complete. This knowledge is essential to discern the limitations of the gyrokinetic simulations of magnetic reconnection when applied to scenarios with moderate guide fields, such as the Solar corona, in contrast to most of the fusion/laboratory plasmas. We extend a previous work by our group, focused in the differences in the macroscopic flows, by analyzing the heating processes and non-thermal features developed by reconnection between both plasma approximations. We relate these processes by identifying some high-frequency cross-streaming instabilities appearing only in the fully kinetic approach. We characterize the effects of these phenonema such as anisotropic electron heating, beam formation and turbulence under different parameter regimes. And finally, we identify the conditions under which these instabilities tends to become negligible in the fully kinetic model, and thus a comparison with gyrokinetic theory becomes more reliable.

  12. Developing new optical imaging techniques for single particle and molecule tracking in live cells

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Wei [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    Differential interference contrast (DIC) microscopy is a far-field as well as wide-field optical imaging technique. Since it is non-invasive and requires no sample staining, DIC microscopy is suitable for tracking the motion of target molecules in live cells without interfering their functions. In addition, high numerical aperture objectives and condensers can be used in DIC microscopy. The depth of focus of DIC is shallow, which gives DIC much better optical sectioning ability than those of phase contrast and dark field microscopies. In this work, DIC was utilized to study dynamic biological processes including endocytosis and intracellular transport in live cells. The suitability of DIC microscopy for single particle tracking in live cells was first demonstrated by using DIC to monitor the entire endocytosis process of one mesoporous silica nanoparticle (MSN) into a live mammalian cell. By taking advantage of the optical sectioning ability of DIC, we recorded the depth profile of the MSN during the endocytosis process. The shape change around the nanoparticle due to the formation of a vesicle was also captured. DIC microscopy was further modified that the sample can be illuminated and imaged at two wavelengths simultaneously. By using the new technique, noble metal nanoparticles with different shapes and sizes were selectively imaged. Among all the examined metal nanoparticles, gold nanoparticles in rod shapes were found to be especially useful. Due to their anisotropic optical properties, gold nanorods showed as diffraction-limited spots with disproportionate bright and dark parts that are strongly dependent on their orientation in the 3D space. Gold nanorods were developed as orientation nanoprobes and were successfully used to report the self-rotation of gliding microtubules on kinesin coated substrates. Gold nanorods were further used to study the rotational motions of cargoes during the endocytosis and intracellular transport processes in live mammalian

  13. Self-assembled HCV core virus-like particles targeted and inhibited tumor cell migration and invasion

    Science.gov (United States)

    Li, Xiang; Xu, Xuehe; Jin, Aihui; Jia, Qunying; Zhou, Huaibin; Kang, Shuai; Lou, Yongliang; Gao, Jimin; Lu, Jianxin

    2013-09-01

    We used a baculovirus expression system to express fusion proteins of HCV core, RGD (Arg-Gly-Asp) peptide, and IFN-α2a fragments in Sf9 cells. Western blotting and electron microscopy demonstrate that HCV core, peptides RGD, and IFN-α2a fusion proteins assemble into 30 to 40 nm nano-particles (virus-like particles, VLPs). Xenograft assays show that VLPs greatly reduced tumor volume and weight with regard to a nontreated xenograft. Migration and invasion results show that VLPs can inhibit the migration and invasion of the breast cancer cells MDA-MB231. This study will provide theoretical and experimental basis for the establishment of safe and effective tumor-targeted drug delivery systems and clinical application of VLPs carrying cell interacting cargo.

  14. Cluster-cluster aggregation with particle replication and chemotaxy: a simple model for the growth of animal cells in culture

    Science.gov (United States)

    Alves, S. G.; Martins, M. L.

    2010-09-01

    Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and in vitro drug testing. In the present paper, a cluster-cluster aggregation model with stochastic particle replication and chemotactically driven motility is investigated as a model for the growth of animal cells in culture. The focus is on the scaling laws governing the aggregation kinetics. Our simulations reveal that in the absence of chemotaxy the mean cluster size and the total number of clusters scale in time as stretched exponentials dependent on the particle replication rate. Also, the dynamical cluster size distribution functions are represented by a scaling relation in which the scaling function involves a stretched exponential of the time. The introduction of chemoattraction among the particles leads to distribution functions decaying as power laws with exponents that decrease in time. The fractal dimensions and size distributions of the simulated clusters are qualitatively discussed in terms of those determined experimentally for several normal and tumoral cell lines growing in culture. It is shown that particle replication and chemotaxy account for the simplest cluster size distributions of cellular aggregates observed in culture.

  15. Natural Mineral Particles Are Cytotoxic to Rainbow Trout Gill Epithelial Cells In Vitro

    OpenAIRE

    Christian Michel; Simon Herzog; Christian de Capitani; Patricia Burkhardt-Holm; Constanze Pietsch

    2014-01-01

    Worldwide increases in fluvial fine sediment are a threat to aquatic animal health. Fluvial fine sediment is always a mixture of particles whose mineralogical composition differs depending on the sediment source and catchment area geology. Nonetheless, whether particle impact in aquatic organisms differs between mineral species remains to be investigated. This study applied an in vitro approach to evaluate cytotoxicity and uptake of four common fluvial mineral particles (quartz, feldspar, mic...

  16. Fluorescent gel particles in the nanometer range for detection of metabolites in living cells

    DEFF Research Database (Denmark)

    Almdal, K.; Sun, H.; Poulsen, A.K.

    2006-01-01

    In this present work a research program that aims at the development of sensor particles based on ratiometric detection of fluorescence from two dyes was embarked on. Such particles can in principle be used to achieve spatially and time resolved measurements of metabolite concentrations in living...... micelles in oil microemulsions. Typical sizes of the particles are tens of nanometers. Characterization methods for such particles based on size exclusion chromatography, photon correlation spectroscopy, scanning electron microscopy, and atomic force microscopy have been developed. The stability...

  17. Biological impact of superparamagnetic iron oxide nanoparticles for magnetic particle imaging of head and neck cancer cells

    Directory of Open Access Journals (Sweden)

    Lindemann A

    2014-10-01

    Full Text Available Antje Lindemann,1 Kerstin Lüdtke-Buzug,2 Bianca M Fräderich,1 Ksenija Gräfe,2 Ralph Pries,1 Barbara Wollenberg11Department of Otorhinolaryngology, University Hospital of Schleswig-Holstein, Luebeck, Germany; 2Institute of Medical Engineering, University of Luebeck, Luebeck, GermanyBackground: As a tomographic imaging technology, magnetic particle imaging (MPI allows high spatial resolution and sensitivity, and the possibility to create real-time images by determining the spatial distribution of magnetic particles. To ensure a prospective biosafe application of UL-D (University of Luebeck-Dextran coated superparamagnetic nanoparticles, we evaluated the biocompatibility of superparamagnetic iron oxide nanoparticles (SPIONs, their impact on biological properties, and their cellular uptake using head and neck squamous cancer cells (HNSCCs.Methods: SPIONs that met specific MPI requirements were synthesized as tracers. Labeling and uptake efficiency were analyzed by hematoxylin and eosin staining and magnetic particle spectrometry. Flow cytometry, 3-(4,5-Dimethylthiazol-2-yl-2,5-diphenyl tetrazolium bromide (MTT assays, and real-time cell analyzer assays were used to investigate apoptosis, proliferation, and the cytokine response of SPION-labeled cells. The production of reactive oxygen species (ROS was determined using a fluorescent dye. Experimental results were compared to the contrast agent Resovist®, a standard agent used in MPI.Results: UL-D nanoparticles and Resovist particles were taken up in vitro by HNSCCs via unspecific phagocytosis followed by cytosolic accumulation. To evaluate toxicity, flow cytometry analysis was performed; results showed that dose- and time-dependent administration of Resovist induced apoptosis whereas cell viability of UL-D-labeled cells was not altered. We observed decreased cell proliferation in response to increased SPION concentrations. An intracellular production of ROS could not be detected, suggesting that

  18. Water Condensation Growth Cells for Ultrafine Particle Collection Onto Concentrated Spots

    Science.gov (United States)

    Lewis, G. S.; Hering, S. V.; Kreisberg, N.

    2007-12-01

    A laminar flow, condensation method, analogous to that employed in the water-based condensation particle counters, is utilized to provide concentrated, low-pressure drop collection of fine and ultrafine particles. With the laminar flow water condensation approach, the aerosol flow is first chilled by a cold walled conditioner, and then introduced into a hot wet-walled condenser. Because water vapor diffuses more rapidly then heat, the air vapor is supersaturated resulting in particles large enough to be collected by impaction. Several types of collectors have been designed and tested. A compact system utilizing a single TED as a heat pump to provide a ~ 25 ° C temperature difference provides collection at 0.4 L/min with a lower cutpoint of 10 nm, a pressure drop of 1 kPa, and a power consumption of 1 Watt. A larger, parallel plate system samples at 10 L/min, and yields a cutpoint of 20 nm. The design of these systems was guided by numeric modeling of the saturation ratios, particle activation and growth. The model includes the heat release from condensation, and the associated warming of the flow that reduces the supersaturation and particle growth at high particle number concentrations. By controlling the system geometry (either plate separation or tube diameter), we are able to activate at small particle sizes while minimizing concentration effects. Our method of particle collection provides a number of other advantages. Particle bounce off the impaction surface can be eliminated by controlling the temperature of the impaction surface so as to maintain a thin film of water on the surface. Particles can also be collected into a small liquid vial containing less then 1 ml of fluid, which eliminates the need for particle extraction from filters or resuspension from surface, it minimizes the total volume of the sample, and it allows for continuous automated collection and analysis.

  19. NUMERICAL STUDY ON THE MIXING OF UNSORTED SEDIMENT PARTICLES DISCHARGED INTO A CROSS-FLOW BY MULTIPHASE PARTICLE-IN-CELL (MP-PIC) METHOD

    Institute of Scientific and Technical Information of China (English)

    Jie GU; Chiwai LI; Hong YANG; Yong ZHAN

    2007-01-01

    The mixing characteristics of dredged sediments of variable size discharged into cross-flow are studied by an Eulerian-Lagrangian method. A three-dimensional (3D) numerical model has been developed by using the modified k-ε parameterization for the turbulence in fluid phase/water and a Lagrangian method for the solid phase/sediments. In the model the wake turbulence induced by sediments has been included as additional source and sink terms in the k-ε model; and the trajectories of the sediments are tracked by the Lagrangian method in which the sediment drift velocities in cross-flow are computed by a multiphase particle-in-cell (MP-PIC) method and the diffusion process is approximated by a random walk model. The hydrodynamic behavior of dumped sediment cloud is governed by the total buoyancy on the cloud, the drag force on each particle and velocity of cross-flow. The cross-flow destroys more or less the double vortices occurred in stagnant ambience and dominates the longitudinal movement of sediment cloud. The computed results suggest satisfactory agreement by comparison with the experimental results of laboratory.

  20. Dissipative particle dynamics simulations of deformation and aggregation of healthy and diseased red blood cells in a tube flow

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Ting; Phan-Thien, Nhan, E-mail: Nhan@nus.edu.sg; Khoo, Boo Cheong; Lim, Chwee Teck [Department of Mechanical Engineering, National University of Singapore, Singapore 119260 (Singapore)

    2014-11-15

    In this paper, we report simulation results assessing the deformation and aggregation of mixed healthy and malaria-infected red blood cells (RBCs) in a tube flow. A three dimensional particle model based on Dissipative Particle Dynamics (DPD) is developed to predict the tube flow containing interacting cells. The cells are also modelled by DPD, with a Morse potential to characterize the cell-cell interaction. As validation tests, a single RBC in a tube flow and two RBCs in a static flow are simulated to examine the cell deformation and intercellular interaction, respectively. The study of two cells, one healthy and the other malaria-infected RBCs in a tube flow demonstrates that the malaria-infected RBC (in the leading position along flow direction) has different effects on the healthy RBC (in the trailing position) at the different stage of parasite development or at the different capillary number. With parasitic development, the malaria-infected RBC gradually loses its deformability, and in turn the corresponding trailing healthy RBC also deforms less due to the intercellular interaction. With increasing capillary number, both the healthy and malaria-infected RBCs are likely to undergo an axisymmetric motion. The minimum intercellular distance becomes small enough so that rouleaux is easily formed, i.e., the healthy and malaria-infected RBCs are difficultly disaggregated.

  1. Alphavirus replicon particles acting as adjuvants promote CD8+ T cell responses to co-delivered antigen.

    Science.gov (United States)

    Thompson, Joseph M; Whitmore, Alan C; Staats, Herman F; Johnston, Robert E

    2008-08-05

    Alphavirus replicon particles induce strong antibody and CD8+ T cell responses to expressed antigens in numerous experimental systems. We have recently demonstrated that Venezuelan equine encephalitis virus replicon particles (VRP) possess adjuvant activity for systemic and mucosal antibody responses. In this report, we demonstrate that VRP induced an increased and balanced serum IgG subtype response to co-delivered antigen, with simultaneous induction of antigen-specific IgG1 and IgG2a antibodies, and increased both systemic and mucosal antigen-specific CD8+ T cell responses, as measured by an IFN-gamma ELISPOT assay. Additionally, VRP further increased antigen-specific T cell immunity in an additive fashion following co-delivery with the TLR ligand, CpG DNA. VRP infection led to recruitment of CD8+ T cells into the mucosal compartment, possibly utilizing the mucosal homing receptor, as this integrin was upregulated on CD8+ T cells in the draining lymph node of VRP-infected animals, where VRP-infected dendritic cells reside. This newly recognized ability of VRP to mediate increased T cell response towards co-delivered antigen provides the potential to both define the molecular basis of alphavirus-induced immunity, and improve alphavirus-based vaccines.

  2. Particle-in-cell simulations of particle energization via shock drift acceleration from low Mach number quasi-perpendicular shocks in solar flares

    CERN Document Server

    Park, Jaehong; Workman, Jared C; Blackman, Eric G

    2012-01-01

    Low Mach number, high beta fast mode shocks can occur in the magnetic reconnection outflows of solar flares. These shocks, which occur above flare loop tops, may provide the electron energization responsible for some of the observed hard X-rays and contemporaneous radio emission. Here we present new 2D particle-in-cell simulations of low Mach number/high beta quasi-perpendicular shocks. The simulations show that electrons above a certain energy threshold experience shock-drift-acceleration. The transition energy between the thermal and non-thermal spectrum and the spectral index from the simulations are consistent with some of the X-ray spectra from RHESSI in the energy regime, $E\\lesssim 40\\sim 100$ keV. Plasma instabilities associated with the shock structure such as the modified-two-stream and the electron whistler/mirror instabilities are examined and compared with the numerical solutions of the kinetic dispersion relations.

  3. Enhanced homologous recombination is induced by alpha-particle radiation in somatic cells of Arabidopsis thaliana

    Science.gov (United States)

    Bian, Po; Liu, Ping; Wu, Yuejin

    Almost 9 percent of cosmic rays which strike the earth's atmosphere are alpha particles. As one of the ionizing radiations (IR), its biological effects have been widely studied. However, the plant genomic instability induced by alpha-particle radiation was not largely known. In this research, the Arabidopsis thaliana transgenic for GUS recombination substrate was used to evaluate the genomic instability induced by alpha-particle radiation (3.3MeV). The pronounced effects of systemic exposure to alpha-particle radiation on the somatic homologous recombination frequency (HRF) were found at different doses. The 10Gy dose of radiation induced the maximal HRF which was 1.9-fold higher than the control. The local radiation of alpha-particle (10Gy) on root also resulted in a 2.5-fold increase of somatic HRF in non-radiated aerial plant, indicating that the signal(s) of genomic instability was transferred to non-radiated parts and initiated their genomic instability. Concurrent treatment of seedlings of Arabidopsis thaliana with alpha-particle and DMSO(ROS scavenger) both in systemic and local radiation signifi- cantly suppressed the somatic HR, indicating that the free radicals produced by alpha-particle radiation took part in the production of signal of genomic instability rather than the signal transfer. Key words: alpha-particle radiation, somatic homologous recombination, genomic instability

  4. Blocking TGF-β expression inhibits silica particle-induced epithelial-mesenchymal transition in human lung epithelial cells.

    Science.gov (United States)

    Rong, Yi; Shen, Yan; Zhang, Zhihong; Cui, Xiuqing; Xiao, Lili; Liu, Yuewei; Luo, Xin; Chen, Weihong

    2015-11-01

    The main characteristic of silicosis is irreversible fibrosis. Certain studies have shown that epithelial-mesenchymal transition (EMT) regulated by transforming growth factor-β (TGF-β) is involved in fibrosis. Thus, we suggest that TGF-β regulated EMT may play an important role in silicosis. In this study, we determined the expression of TGF-β-Smad2/3, EMT- and ECM-related markers in lung epithelial cells treated with silica particle by RT-PCR, western-blot and ELISA. In order to explore the role of TGF-β, we used TGF-β inhibitor in the cell model. We found that the cells lost the expression of epithelial phenotypic markers and acquired increased expression of mesenchymal cells markers with ECM deposition after treatment with silica particle. Moreover, the changes of EMT-related event was restricted in response to TGF-β inhibitor. These findings suggest that EMT is essentially involved in the pathogenesis of fibrosis induced by silica particles and down-regulating the TGF-β expression can inhibit the process of EMT.

  5. HIV-derived lentiviral particles promote T-cell independent activation and differentiation of naïve cognate conventional B2-cells in vitro.

    Science.gov (United States)

    Gardt, Oliver; Grewe, Bastian; Tippler, Bettina G; Überla, Klaus; Temchura, Vladimir V

    2013-10-17

    In animal models, lentiviral particles (LP) were shown to be promising HIV vaccine candidates. Since little is known about the direct impact of LP on antigen-specific B cells, we incorporated Hen Egg Lysozyme (HEL) into LP (HEL-LP) derived from HIV to study their effect on HEL-specific, B cell receptor-transgenic B-cells (HEL(+)B-cells) in vitro. We observed preferential binding of HEL-LP to HEL(+)B-cells and their efficient internalization. HEL-LP were able to effectively cross-link B-cell receptors as indicated by the loss of surface CD62L. In the absence of CD4(+) T-cells, other activation events induced by LP in cognate naïve B-cells included increased expression of activation and co-stimulatory molecules as well as an enhanced proliferative response. Additionally, the B-cell phenotype shifted toward a germinal center pattern with further differentiation into memory and IgG3- and IgA-producing cells. The observed CD4(+) T-cell independent activation and differentiation may be due to LP-induced expression of CD40L by a subset of cognate B-cells. Thus, even in the absence of CD4(+) T-cells LP provide strong direct activation signals to cognate naïve B-cells, which may contribute to the strong humoral immune responses observed after LP immunization. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Expression of CXCR4 in cord blood-derived CD133+ cells treated with platelet micro-particles.

    Science.gov (United States)

    Moghaddam, Farzaneh; Oodi, Arezoo; Nikougoftar Zarif, Mahin; Amani, Maryam; Amirizadeh, Naser

    2016-11-01

    Platelet micro-particles (MPs) contain CXCR4 markers and are able to transfer them into hematopoietic stem cells. Therefore, effect of platelet MPs (PMPs) on the expression levels of CXCR4 and CD34 markers in these cells was examined. Isolated CD 133+ cells cultivated for 5 d in the stem span medium and PMPs. Fold increase of CD34+ cells in the presence of 5 and 10 g/ml of PMPs was increased significantly. CXCR4+ cell percent in the presence of 10 g/ml PMPs compared with control cells (63.8 ± 6.4) was increased (P < 0.05). PMPs were no affect on clonogenicity of hematopoietic progenitor cells. Cord blood CD133+ cells are able to maintain long-term hematopoiesis and to differentiate to hematopoietic lineages. CXCR4 over expression is involved in homing and successful transplantation of hematopoietic stem cells (HSCs) in the bone marrow. PMPs contain CXCR4 markers and are able to transfer them into hematopoietic stem cells. Therefore, considering the importance of CD133+ cells as primitive HSCs, the effect of PMPs on the expression levels of CXCR4 and CD34 markers in these cells was examined. Cord blood CD133+ cells were isolated by MACS. Isolated cells were divided into three groups: (i) control cells, (ii) cells treated with 5 μg/ml PMPs, (iii) cells treated with 10 μg/ml PMPs. Cells were cultivated for 5 d in the stem span medium. Expression of CD 133, CD34, and CXCR4 surface marker was analyzed by flow cytometry. Total cell numbers were counted by hemocytometer and clonogenicity were measured by colony assay. PMPs were no effect on CD133+ cells proliferation, but fold increase of CD34+ cells in the presence of 5 and 10 g/ml of PMPs was increased significantly. CXCR4+ cell percent in the presence of 10 g/ml PMPs compared with control cells (63.8 ± 6.4) was increased (P < 0.05). PMPs were no affect on clonogenicity of hematopoietic progenitor cells. Exposure of CD133+ cells isolated from cord blood to PMPs with 10

  7. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    CERN Document Server

    Xiao, Jianyuan; Liu, Jian; He, Yang; Zhang, Ruili; Sun, Yajuan

    2015-01-01

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithm conserves a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially-discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a splitting method discovered by He et al., which produces five exactly-soluable sub-systems, and high-order structure- preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom ...

  8. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jianyuan [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Qin, Hong [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543, USA; Liu, Jian [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; He, Yang [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Zhang, Ruili [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Sun, Yajuan [LSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, P.O. Box 2719, Beijing 100190, China

    2015-11-01

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint arXiv: 1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave. (C) 2015 AIP Publishing LLC.

  9. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jianyuan; Liu, Jian; He, Yang; Zhang, Ruili [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026 (China); Qin, Hong, E-mail: hongqin@ustc.edu.cn [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Sun, Yajuan [LSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, P.O. Box 2719, Beijing 100190 (China)

    2015-11-15

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint http://arxiv.org/abs/arXiv:1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave.

  10. The Effects of Crystal Phase and Particle Morphology of Calcium Phosphates on Proliferation and Differentiation of Human Mesenchymal Stromal Cells.

    Science.gov (United States)

    Danoux, Charlène; Pereira, Daniel; Döbelin, Nicola; Stähli, Christoph; Barralet, Jake; van Blitterswijk, Clemens; Habibovic, Pamela

    2016-07-01

    Calcium phosphate (CaP) ceramics are extensively used for bone regeneration; however, their clinical performance is still considered inferior to that of patient's own bone. To improve the performance of CaP bone graft substitutes, it is important to understand the effects of their individual properties on a biological response. The aim of this study is to investigate the effects of the crystal phase and particle morphology on the behavior of human mesenchymal stromal cells (hMSCs). To study the effect of the crystal phase, brushite, monetite, and octacalcium phosphate (OCP) are produced by controlling the precipitation conditions. Brushite and monetite are produced as plate-shaped and as needle-shaped particles, to further investigate the effect of particle morphology. Proliferation of hMSCs is inhibited on OCP as compared to brushite and monetite in either morphology. Brushite needles consistently show the lowest expression of most osteogenic markers, whereas the expression on OCP is in general high. There is a trend toward a higher expression of the osteogenic markers on plate-shaped than on needle-shaped particles for both brushite and monetite. Within the limits of CaP precipitation, these data indicate the effect of both crystal phase and particle morphology of CaPs on the behavior of hMSCs.

  11. Intermittent contact of fluidized anode particles containing exoelectrogenic biofilms for continuous power generation in microbial fuel cells

    KAUST Repository

    Liu, Jia

    2014-09-01

    Current generation in a microbial fuel cell can be limited by the amount of anode surface area available for biofilm formation, and slow substrate degradation kinetics. Increasing the anode surface area can increase the amount of biofilm, but performance will improve only if the anode material is located near the cathode to minimize solution internal resistance. Here we demonstrate that biofilms do not have to be in constant contact with the anode to produce current in an MFC. Granular activated carbon particles enriched with exoelectrogenic biofilm are fluidized (by stirring) in the anode chamber of the MFC, resulting in only intermittent contact between the particles and the anode current collector. The maximum power density generated is 951 ± 10 mW m-2, compared to 813 ± 2 mW m-2 for the control without stirring (packed bed), and 525 ± 1 mW m-2 in the absence of GAC particles and without stirring. GAC-biofilm particles demonstrate capacitor-like behavior, but achieve nearly constant discharge conditions due to the large number of particles that contact the current collector. These results provide proof of concept for the development of flowable electrode reactors, where anode biofilms can be electrically charged in a separate storage tank and then rapidly discharged in compact anode chambers. © 2014 Elsevier B.V. All rights reserved.

  12. Biological Effects of Particles with Very High Energy Deposition on Mammalian Cells Utilizing the Brookhaven Tandem Van de Graaff Accelerator

    Science.gov (United States)

    Saha, Janapriya; Cucinotta, Francis A.; Wang, Minli

    2013-01-01

    High LET radiation from GCR (Galactic Cosmic Rays) consisting mainly of high charge and energy (HZE) nuclei and secondary protons and neutrons, and secondaries from protons in SPE (Solar Particle Event) pose a major health risk to astronauts due to induction of DNA damage and oxidative stress. Experiments with high energy particles mimicking the space environment for estimation of radiation risk are being performed at NASA Space Radiation Laboratory at BNL. Experiments with low energy particles comparing to high energy particles of similar LET are of interest for investigation of the role of track structure on biological effects. For this purpose, we report results utilizing the Tandem Van de Graaff accelerator at BNL. The primary objective of our studies is to elucidate the influence of high vs low energy deposition on track structure, delta ray contribution and resulting biological responses. These low energy ions are of special relevance as these energies may occur following absorption through the spacecraft and shielding materials in human tissues and nuclear fragments produced in tissues by high energy protons and neutrons. This study will help to verify the efficiency of these low energy particles and better understand how various cell types respond to them.

  13. Heterogeneous uptake and reactivity of formic acid on calcium carbonate particles: a Knudsen cell reactor, FTIR and SEM study.

    Science.gov (United States)

    Al-Hosney, Hashim A; Carlos-Cuellar, Sofia; Baltrusaitis, Jonas; Grassian, Vicki H

    2005-10-21

    The heterogeneous uptake and reactivity of formic acid (HCOOH), a common gas-phase organic acid found in the environment, on calcium carbonate (CaCO(3)) particles have been investigated using a Knudsen cell reactor, Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM). FTIR measurements show that the adsorption of formic acid on the surface of calcium carbonate results in the formation of calcium formate. Besides calcium formate, carbonic acid is also a reaction product under dry conditions (dry conditions and at low pressures, the initial uptake coefficient of formic acid on CaCO(3) particles is measured to be 3 +/- 1 x 10(-3) and decreases as the surface saturates with adsorbed products. The maximum surface coverage of formic acid under dry conditions is determined to be (3 +/- 1)x 10(14) molecules cm(-2). Under humidified conditions (RH >10%), adsorbed water on the surface of the carbonate particles participates in the surface reactivity of these particles, which results in the enhanced uptake kinetics and extent of reaction of this organic acid on CaCO(3) as well as opens up several new reaction pathways. These reaction pathways include: (i) the water-assisted dissociation of carbonic acid to CO(2) and H(2)O and (ii) the formation of calcium formate islands and crystallites, as evident by SEM images. The results presented here show that adsorbed water plays a potentially important role in the surface chemistry of gas-phase organic acids on calcium carbonate particles.

  14. An electrostatic particle-in-cell model for a lower hybrid grill

    Energy Technology Data Exchange (ETDEWEB)

    Rantamaeki, K

    1998-07-01

    In recent lower hybrid (LH) current drive experiments, generation of hot spots and impurities in the grill region have been observed on Tore Supra and Tokamak de Varennes (TdeV). A possible explanation is the parasitic absorption of the LH power in front of the grill. In parasitic absorption, the short-wavelength part of the lower hybrid spectrum can resonantly interact with the cold edge electrons. In this work, the absorption of the LH waves and the generation of fast electrons near the waveguide mouth is investigated with a new tool in this context: particle-in-cell (PIC) simulations. The advantage of this new method is that the electric field is calculated self-consistently. The PIC simulations also provide the key parameters for the hot spot problem: the absorbed power, the radial deposition profiles and the absorption length. A grill model has been added to the 2d3v PIC code XPDP2. Two sets of simulations were made. The first simulations used a phenomenological grill model. Strong absorption in the edge plasma was obtained. About 5% of the coupled power was absorbed within 1.7 mm in the case with fairly large amount of power in the modes with large parallel refractive index. Consequently, a rapid generation of fast electrons took place in the same region. In order to model experiments with realistic wave spectra, the PIC code was coupled to the slow wave antenna coupling code SWAN. The absorption within 1.7 mm in front of the grill was found to be between 2 and 5%. In the short time of a few wave periods, part of the initially thermal electrons (T{sub e} = 100 eV) were accelerated to velocities corresponding to a few keV. (orig.)

  15. Particle-in-cell modeling for MJ scale dense plasma focus with varied anode shape

    Energy Technology Data Exchange (ETDEWEB)

    Link, A., E-mail: link6@llnl.gov; Halvorson, C., E-mail: link6@llnl.gov; Schmidt, A. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Hagen, E. C. [National Security Technologies, Las Vegas, NV 89030 (United States); Rose, D. V.; Welch, D. R. [Voss Scientific LLC, Albuquerque NM 87108 (United States)

    2014-12-15

    Megajoule scale dense plasma focus (DPF) Z-pinches with deuterium gas fill are compact devices capable of producing 10{sup 12} neutrons per shot but past predictive models of large-scale DPF have not included kinetic effects such as ion beam formation or anomalous resistivity. We report on progress of developing a predictive DPF model by extending our 2D axisymmetric collisional kinetic particle-in-cell (PIC) simulations from the 4 kJ, 200 kA LLNL DPF to 1 MJ, 2 MA Gemini DPF using the PIC code LSP. These new simulations incorporate electrodes, an external pulsed-power driver circuit, and model the plasma from insulator lift-off through the pinch phase. To accommodate the vast range of relevant spatial and temporal scales involved in the Gemini DPF within the available computational resources, the simulations were performed using a new hybrid fluid-to-kinetic model. This new approach allows single simulations to begin in an electron/ion fluid mode from insulator lift-off through the 5-6 μs run-down of the 50+ cm anode, then transition to a fully kinetic PIC description during the run-in phase, when the current sheath is 2-3 mm from the central axis of the anode. Simulations are advanced through the final pinch phase using an adaptive variable time-step to capture the fs and sub-mm scales of the kinetic instabilities involved in the ion beam formation and neutron production. Validation assessments are being performed using a variety of different anode shapes, comparing against experimental measurements of neutron yield, neutron anisotropy and ion beam production.

  16. Particle-in-cell simulations of electron beam control using an inductive current divider

    Energy Technology Data Exchange (ETDEWEB)

    Swanekamp, S. B.; Angus, J. R.; Cooperstein, G.; Ottinger, P. F.; Richardson, A. S.; Schumer, J. W.; Weber, B. V. [Plasma Physics Division, Naval Research Laboratory, Washington, District of Columbia 20375 (United States)

    2015-11-15

    Kinetic, time-dependent, electromagnetic, particle-in-cell simulations of the inductive current divider are presented. The inductive current divider is a passive method for controlling the trajectory of an intense, hollow electron beam using a vacuum structure that inductively splits the beam's return current. The current divider concept was proposed and studied theoretically in a previous publication [Swanekamp et al., Phys. Plasmas 22, 023107 (2015)]. A central post carries a portion of the return current (I{sub 1}), while the outer conductor carries the remainder (I{sub 2}) with the injected beam current given by I{sub b} = I{sub 1} + I{sub 2}. The simulations are in agreement with the theory which predicts that the total force on the beam trajectory is proportional to (I{sub 2}−I{sub 1}) and the force on the beam envelope is proportional to I{sub b}. Independent control over both the current density and the beam angle at the target is possible by choosing the appropriate current-divider geometry. The root-mean-square (RMS) beam emittance (ε{sub RMS}) varies as the beam propagates through the current divider to the target. For applications where control of the beam trajectory is desired and the current density at the target is similar to the current density at the entrance foil, there is a modest 20% increase in ε{sub RMS} at the target. For other applications where the beam is pinched to a current density ∼5 times larger at the target, ε{sub RMS} is 2–3 times larger at the target.

  17. Particle-in-cell simulations of the relaxation of electron beams in inhomogeneous solar wind plasmas

    Science.gov (United States)

    Thurgood, Jonathan O.; Tsiklauri, David

    2016-12-01

    Previous theoretical considerations of electron beam relaxation in inhomogeneous plasmas have indicated that the effects of the irregular solar wind may account for the poor agreement of homogeneous modelling with the observations. Quasi-linear theory and Hamiltonian models based on Zakharov's equations have indicated that when the level of density fluctuations is above a given threshold, density irregularities act to de-resonate the beam-plasma interaction, restricting Langmuir wave growth on the expense of beam energy. This work presents the first fully kinetic particle-in-cell (PIC) simulations of beam relaxation under the influence of density irregularities. We aim to independently determine the influence of background inhomogeneity on the beam-plasma system, and to test theoretical predictions and alternative models using a fully kinetic treatment. We carry out one-dimensional (1-D) PIC simulations of a bump-on-tail unstable electron beam in the presence of increasing levels of background inhomogeneity using the fully electromagnetic, relativistic EPOCH PIC code. We find that in the case of homogeneous background plasma density, Langmuir wave packets are generated at the resonant condition and then quasi-linear relaxation leads to a dynamic increase of wavenumbers generated. No electron acceleration is seen - unlike in the inhomogeneous experiments, all of which produce high-energy electrons. For the inhomogeneous experiments we also observe the generation of backwards-propagating Langmuir waves, which is shown directly to be due to the refraction of the packets off the density gradients. In the case of higher-amplitude density fluctuations, similar features to the weaker cases are found, but also packets can also deviate from the expected dispersion curve in -space due to nonlinearity. Our fully kinetic PIC simulations broadly confirm the findings of quasi-linear theory and the Hamiltonian model based on Zakharov's equations. Strong density fluctuations

  18. Effects of apatite particle size in two apatite/collagen composites on the osteogenic differentiation profile of osteoblastic cells.

    Science.gov (United States)

    Hatakeyama, Wataru; Taira, Masayuki; Chosa, Naoyuki; Kihara, Hidemichi; Ishisaki, Akira; Kondo, Hisatomo

    2013-12-01

    The development of new osteoconductive bone substitute materials is expected in medicine. In this study, we attempted to produce new hydroxylapatite (HAP)/collagen (Col) composites using two HAP particles of different sizes and porcine type I collagen. The two HAP particles were either nano-sized (40 nm in average diameter; n-HAP) or had macro-pore sizes of 0.5‑1.0 mm in length with fully interconnected pores (m-HAP). The aim of this study was to investigate the effects of apatite particle size in two HAP/Col composites on the osteogenic differentiation profile in osteoblast-like cells (SaOS-2). We created a collagen control sponge (Col) and two HAP/Col composite sponges (n-HAP/Col and m-HAP/Col) using freeze-drying and dehydrothermal cross-linking techniques, and then punched out samples of 6 mm in diameter and 1 mm in height. The SaOS-2 cells were cultured on three test materials for 1, 2, 3 and 4 weeks. Total RNA was extracted from the cultured cells and the expression of osteogenic differentiation-related genes was evaluated by reverse transcription PCR (RT-PCR) using primer sets of alkaline phosphatase (ALP), type 1 collagen (COL1), bone sialoprotein (BSP) and osteocalcin precursor [bone gamma-carboxyglutamate (gla) protein (BGLAP)] genes, as well as the β-actin gene. The cells were also cultured on Col, n-HAP/Col and m-HAP/Col specimens for 1 and 4 weeks, and were then observed under a scanning electron microscope (SEM). The experimental results were as follows: RT-PCR indicated that osteogenic differentiation, particularly the gene expression of BSP, was most accelerated when the cells were cultured on n-HAP/Col specimens, followed by m-HAP/Col, whilst the weakest accelaeration was observed when the cells were cultured on Col specimens. As shown by the SEM images, the SaOS-2 cells were fibroblastic when cultured on Col specimens for up to 4 weeks; they were fibroblastic when cultured on n-HAP/Col specimens for 1 week, but appeared as spheroids

  19. Data on the histological and immune cell response in the popliteal lymph node in mice following exposure to metal particles and ions.

    Science.gov (United States)

    Winans, Bethany; Tvermoes, Brooke E; Unice, Kenneth M; Kovochich, Michael; Fung, Ernest S; Christian, Whitney V; Donovan, Ellen; Finley, Brent L; Kimber, Ian; Paustenbach, Dennis J

    2016-12-01

    Hip implants containing cobalt-chromium (CoCr) have been used for over 80 years. In patients with metal-on-metal (MoM) hip implants, it has been suggested that wear debris particles may contribute to metal sensitization in some individuals, leading to adverse reactions. This article presents data from a study in which the popliteal lymph node assay (PLNA) was used to assess immune responses in mice treated with chromium-oxide (Cr2O3) particles, metal salts (CoCl2, CrCl3, and NiCl2) or Cr2O3 particles with metal salts ("A preliminary evaluation of immune stimulation following exposure to metal particles and ions using the mouse popliteal lymph node assay" (B.E. Tvermoes, K.M. Unice, B. Winans, M. Kovochich, E.S. Fung, W.V. Christian, E. Donovan, B.L. Finley, B.L. Kimber, I. Kimber, D.J. Paustenbach, 2016) [1]). Data are presented on (1) the chemical characterization of TiO2 particles (used as a particle control), (2) clinical observations in mice treated with Cr2O3 particles, metal salts or Cr2O3 particles with metal salts, (3) PLN weight and weight index (WI) in mice treated with Cr2O3 particles, metal salts or Cr2O3 particles with metal salts, (4) histological changes in PLNs of mice treated with Cr2O3 particles, metal salts or Cr2O3 particles with metal salts, (5) percentages of immune cells in the PLNs of mice treated with Cr2O3 particles, metal salts or Cr2O3 particles with metal salts, and (6) percentages of proliferating cells in the PLNs of mice treated with Cr2O3 particles, metal salts or Cr2O3 particles with metal salts.

  20. Brownian Dynamics of a Suspension of Particles with Constrained Voronoi Cell Volumes

    KAUST Repository

    Singh, John P.

    2015-06-23

    © 2015 American Chemical Society. Solvent-free polymer-grafted nanoparticle fluids consist of inorganic core particles fluidized by polymers tethered to their surfaces. The attachment of the suspending fluid to the particle surface creates a strong penalty for local variations in the fluid volume surrounding the particles. As a model of such a suspension we perform Brownian dynamics of an equilibrium system consisting of hard spheres which experience a many-particle potential proportional to the variance of the Voronoi volumes surrounding each particle (E = α(Vi-V0)2). The coefficient of proportionality α can be varied such that pure hard sphere dynamics is recovered as α → 0, while an incompressible array of hairy particles is obtained as α →. As α is increased the distribution of Voronoi volumes becomes narrower, the mean coordination number of the particle increases and the variance in the number of nearest neighbors decreases. The nearest neighbor peaks in the pair distribution function are suppressed and shifted to larger radial separations as the constraint acts to maintain relatively uniform interstitial regions. The structure factor of the model suspension satisfies S(k=0) → 0 as α → in accordance with expectation for a single component (particle plus tethered fluid) incompressible system. The tracer diffusivity of the particles is reduced by the volume constraint and goes to zero at φ 0.52, indicating an earlier glass transition than has been observed in hard sphere suspensions. The total pressure of the suspension grows in proportion to (αkBT)1/2 as the strength of the volume-constraint potential grows. This stress arises primarily from the interparticle potential forces, while the hard-sphere collisional contribution to the stress is suppressed by the volume constraint.

  1. Brownian Dynamics of a Suspension of Particles with Constrained Voronoi Cell Volumes.

    Science.gov (United States)

    Singh, John P; Walsh, Stuart D C; Koch, Donald L

    2015-06-23

    Solvent-free polymer-grafted nanoparticle fluids consist of inorganic core particles fluidized by polymers tethered to their surfaces. The attachment of the suspending fluid to the particle surface creates a strong penalty for local variations in the fluid volume surrounding the particles. As a model of such a suspension we perform Brownian dynamics of an equilibrium system consisting of hard spheres which experience a many-particle potential proportional to the variance of the Voronoi volumes surrounding each particle (E = α(Vi-V0)(2)). The coefficient of proportionality α can be varied such that pure hard sphere dynamics is recovered as α → 0, while an incompressible array of hairy particles is obtained as α → ∞. As α is increased the distribution of Voronoi volumes becomes narrower, the mean coordination number of the particle increases and the variance in the number of nearest neighbors decreases. The nearest neighbor peaks in the pair distribution function are suppressed and shifted to larger radial separations as the constraint acts to maintain relatively uniform interstitial regions. The structure factor of the model suspension satisfies S(k=0) → 0 as α → ∞ in accordance with expectation for a single component (particle plus tethered fluid) incompressible system. The tracer diffusivity of the particles is reduced by the volume constraint and goes to zero at ϕ ∼ 0.52, indicating an earlier glass transition than has been observed in hard sphere suspensions. The total pressure of the suspension grows in proportion to (αkBT)(1/2) as the strength of the volume-constraint potential grows. This stress arises primarily from the interparticle potential forces, while the hard-sphere collisional contribution to the stress is suppressed by the volume constraint.

  2. The Plasma Simulation Code: A modern particle-in-cell code with load-balancing and GPU support

    CERN Document Server

    Germaschewski, Kai; Ahmadi, Narges; Wang, Liang; Abbott, Stephen; Ruhl, Hartmut; Bhattacharjee, Amitava

    2013-01-01

    Recent increases in supercomputing power, driven by the multi-core revolution and accelerators such as the IBM Cell processor, graphics processing units (GPUs) and Intel's Many Integrated Core (MIC) technology have enabled kinetic simulations of plasmas at unprecedented resolutions, but changing HPC architectures also come with challenges for writing efficient numerical codes. This paper describes the Plasma Simulation Code (PSC), an explicit, electromagnetic particle-in-cell code with support for different order particle shape functions. We focus on two distinguishing feature of the code: patch-based load balancing using space-filling curves, and support for Nvidia GPUs, which achieves substantial speed-up of up to more than 6x on the Cray XK7 architecture compared to a CPU-only implementation.

  3. Monte-Carlo approach to calculate the ionization of warm dense matter within particle-in-cell simulations

    CERN Document Server

    Wu, D; Yu, W; Fritzsche, S

    2016-01-01

    A physical model based on Monte-Carlo approach is proposed to calculate the ionization dynamics of warm dense matters within particle-in-cell simulations, where impact ionization, electron-ion recombination and ionization potential depression (IPD) by surrounding plasmas are taken into consideration self-consistently. When compared with other models, which are applied in the literature for plasmas near thermal equilibrium, the temporal relaxation of ionizations can also be simulated by the proposed model with the final thermal equilibrium determined by the competition between impact ionization and its inverse process, i.e., electron-ion recombination. Our model is general and can be applied for both single elements and alloys with quite different compositions. The proposed model is implemented into a particle-in-cell (PIC) simulation code, and the average ionization degree of bulk aluminium varying with temperature is calculated, showing good agreement with the data provided by FLYCHK code.

  4. Characterization of native 40 S particles from Krebs II mouse ascites tumor cells: resolution, nomenclature and molecular weights of the nonribosomal proteins

    DEFF Research Database (Denmark)

    Reichert, G; Issinger, O G

    1981-01-01

    Native 40 S particles from Krebs II mouse ascites tumor cells were isolated on a large scale. A nonribosomal protein moiety of about 30 proteins could be removed from the ribosomal particles by treatment with 250 mM KCl. These proteins were analysed by two-dimensional polyacrylamide gel electroph......Native 40 S particles from Krebs II mouse ascites tumor cells were isolated on a large scale. A nonribosomal protein moiety of about 30 proteins could be removed from the ribosomal particles by treatment with 250 mM KCl. These proteins were analysed by two-dimensional polyacrylamide gel...

  5. Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS

    DEFF Research Database (Denmark)

    Lagerholm, B. Christoffer; Andrade, Débora M.; Clausen, Mathias P.

    2017-01-01

    Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diff...... embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of ≈0.7-1.0 μm2 s-1, and a compartment size of about 100-150 nm....

  6. Infected dendritic cells are sufficient to mediate the adjuvant activity generated by Venezuelan equine encephalitis virus replicon particles.

    Science.gov (United States)

    Tonkin, Daniel R; Whitmore, Alan; Johnston, Robert E; Barro, Mario

    2012-06-22

    Replicon particles derived from Venezuelan equine encephalitis virus (VEE) are infectious non-propagating particles which act as a safe and potent systemic, mucosal, and cellular adjuvant when delivered with antigen. VEE and VEE replicon particles (VRP) can target multiple cell types including dendritic cells (DCs). The role of these cell types in VRP adjuvant activity has not been previously evaluated, and for these studies we focused on the contribution of DCs to the response to VRP. By analysis of VRP targeting in the draining lymph node, we found that VRP induced rapid recruitment of TNF-secreting monocyte-derived inflammatory dendritic cells. VRP preferentially infected these inflammatory DCs as well as classical DCs and macrophages, with less efficient infection of other cell types. DC depletion suggested that the interaction of VRP with classical DCs was required for recruitment of inflammatory DCs, induction of high levels of many cytokines, and for stable transport of VRP to the draining lymph node. Additionally, in vitro-infected DCs enhanced antigen-specific responses by CD4 and CD8 T cells. By transfer of VRP-infected DCs into mice we showed that these DCs generated an inflammatory state in the draining lymph node similar to that achieved by VRP injection. Most importantly, VRP-infected DCs were sufficient to establish robust adjuvant activity in mice comparable to that produced by VRP injection. These findings indicate that VRP infect, recruit and activate both classical and inflammatory DCs, and those DCs become mediators of the VRP adjuvant activity. Published by Elsevier Ltd.

  7. DIESEL EXHAUST PARTICLES INDUCE ABERRANT ALVEOLAR EPITHELIAL DIRECTED CELL MOVEMENT BY DISRUPTION OF POLARITY MECHANISMS

    Science.gov (United States)

    Disruption of the respiratory epithelium contributes to the progression of a variety of respiratory diseases that are aggravated by exposure to air pollutants, specifically traffic-based pollutants such as diesel exhaust particles (DEP). Recognizing that lung repair following inj...

  8. Genomic Profiling of a Human Leukemic Monocytic Cell-Line (THP-1 Exposed to Alpha Particle Radiation

    Directory of Open Access Journals (Sweden)

    Vinita Chauhan

    2012-01-01

    Full Text Available This study examined alpha (α- particle radiation effects on global changes in gene expression in human leukemic monocytic cells (THP-1 for the purposes of mining for candidate biomarkers that could be used for the development of a biological assessment tool. THP-1 cells were exposed to α-particle radiation at a dose range of 0 to 1.5 Gy. Twenty-four hours and three days after exposure gene expression was monitored using microarray technology. A total of 16 genes were dose responsive and classified as early onset due to their expression 24 h after exposure. Forty-eight transcripts were dose responsive and classified as late-onset as they were expressed 72 h after exposure. Among these genes, 6 genes were time and dose responsive and validated further using alternate technology. These transcripts were upregulated and associated with biological processes related to immune function, organelle stability and cell signalling/communication. This panel of genes merits further validation to determine if they are strong candidate biomarkers indicative of α-particle exposure.

  9. The radiobiology of laser-driven particle beams: focus on sub-lethal responses of normal human cells

    Science.gov (United States)

    Manti, L.; Perozziello, F. M.; Borghesi, M.; Candiano, G.; Chaudhary, P.; Cirrone, G. A. P.; Doria, D.; Gwynne, D.; Leanza, R.; Prise, K. M.; Romagnani, L.; Romano, F.; Scuderi, V.; Tramontana, A.

    2017-03-01

    Accelerated proton beams have become increasingly common for treating cancer. The need for cost and size reduction of particle accelerating machines has led to the pioneering investigation of optical ion acceleration techniques based on laser-plasma interactions as a possible alternative. Laser-matter interaction can produce extremely pulsed particle bursts of ultra-high dose rates (>= 109 Gy/s), largely exceeding those currently used in conventional proton therapy. Since biological effects of ionizing radiation are strongly affected by the spatio-temporal distribution of DNA-damaging events, the unprecedented physical features of such beams may modify cellular and tissue radiosensitivity to unexplored extents. Hence, clinical applications of laser-generated particles need thorough assessment of their radiobiological effectiveness. To date, the majority of studies have either used rodent cell lines or have focussed on cancer cell killing being local tumour control the main objective of radiotherapy. Conversely, very little data exist on sub-lethal cellular effects, of relevance to normal tissue integrity and secondary cancers, such as premature cellular senescence. Here, we discuss ultra-high dose rate radiobiology and present preliminary data obtained in normal human cells following irradiation by laser-accelerated protons at the LULI PICO2000 facility at Laser Lab Europe, France.

  10. Studying the cytotoxicity and oxidative stress induced by two kinds of bentonite particles on human B lymphoblast cells in vitro.

    Science.gov (United States)

    Zhang, Meibian; Lu, Yezhen; Li, Xiaoxue; Chen, Qing; Lu, Longxi; Xing, Mingluan; Zou, Hua; He, Jiliang

    2010-02-12

    The aim of the present study was to evaluate the cytotoxicity and oxidative stress induced by native and active bentonite particles (BPs) on human B lymphoblast cells using seven assays. Our results showed that the order of cytotoxicity was: active BPs>native BPs>quartz particles (DQ-12)>gypsum, according to the IC50 values in CCK-8 assay and neutral red uptake (NRU) assay. The lactate dehydrogenase (LDH) leakage, the proportions of early apoptotic cells, the reactive oxygen species (ROS) generation, the superoxide dismutase (SOD) inhibition and the malondialdehyde (MDA) release in the native and active BPs groups were significantly higher than those in the gypsum and DQ-12 groups (Pstress induced by active BPs was significantly higher than that induced by native BPs (Pstress on human B lymphoblast cells in vitro. The cytotoxic difference between active BPs and native BPs may be associated with the adsorption capacity of BPs and oxidative stress induced by BPs to a certain extent. The insoluble particle fractions may play a main role in the cytotoxic effects and oxidative stress induced by BPs.

  11. [Characterization of hepatitis C virus structural proteins and HCV-like particles produced in recombinant baculovirus infected insect cells].

    Science.gov (United States)

    Belzhelarskaia, S N; Koroleva, N N; Popenko, V V; Drutsa, V L; Orlova, O V; Rubtsov, P M; Kochetkov, S N

    2010-01-01

    Three proteins, namely: "core" protein C and glycoproteins E1 and E2, are main structural proteins forming a hepatitis C vius (HCV) virion. The virus structure and assembly, a role of the structural proteins in virion morphogenesis remain unknown because of the lack of an efficient culture system for HCV to be grown in vitro. Using recombinant baculoviruses expressing HCV structural protein genes in insect cells the specific structural proteins at the level of 25-35% relative to a common cell protein content, heterodimers of the glcoproteins, and HCV-like particles have been obtained. It has been demonstrated that recombinant proteins C, E1, and E2 go through the posttranslation modification, the glycoproteins form the non-covalent heterodimer, and HCV-like particles are located in endoplasmatic reticulum membrains of infected cells. An ability of the expressed proteins for forming E1E2 dimers and HCV-like particles was used for studying the role of E1 protein glcosylation upon expression and processing of the glycoproteins.

  12. Cytotoxicity and genotoxicity of nanosized and microsized titanium dioxide and iron oxide particles in Syrian hamster embryo cells.

    Science.gov (United States)

    Guichard, Yves; Schmit, Julien; Darne, Christian; Gaté, Laurent; Goutet, Michèle; Rousset, Davy; Rastoix, Olivier; Wrobel, Richard; Witschger, Olivier; Martin, Aurélie; Fierro, Vanessa; Binet, Stéphane

    2012-07-01

    Potential differences in the toxicological properties of nanosized and non-nanosized particles have been notably pointed out for titanium dioxide (TiO(2)) particles, which are currently widely produced and used in many industrial areas. Nanoparticles of the iron oxides magnetite (Fe(3)O(4)) and hematite (Fe(2)O(3)) also have many industrial applications but their toxicological properties are less documented than those of TiO(2). In the present study, the in vitro cytotoxicity and genotoxicity of commercially available nanosized and microsized anatase TiO(2), rutile TiO(2), Fe(3)O(4), and Fe(2)O(3) particles were compared in Syrian hamster embryo (SHE) cells. Samples were characterized for chemical composition, primary particle size, crystal phase, shape, and specific surface area. In acellular assays, TiO(2) and iron oxide particles were able to generate reactive oxygen species (ROS). At the same mass dose, all nanoparticles produced higher levels of ROS than their microsized counterparts. Measurement of particle size in the SHE culture medium showed that primary nanoparticles and microparticles are present in the form of micrometric agglomerates of highly poly-dispersed size. Uptake of primary particles and agglomerates by SHE exposed for 24 h was observed for all samples. TiO(2) samples were found to be more cytotoxic than iron oxide samples. Concerning primary size effects, anatase TiO(2), rutile TiO(2), and Fe(2)O(3) nanoparticles induced higher cytotoxicity than their microsized counterparts after 72 h of exposure. Over this treatment time, anatase TiO(2) and Fe(2)O(3) nanoparticles also produced more intracellular ROS compared to the microsized particles. However, similar levels of DNA damage were observed in the comet assay after 24 h of exposure to anatase nanoparticles and microparticles. Rutile microparticles were found to induce more DNA damage than the nanosized particles. However, no significant increase in DNA damage was detected from nanosized and

  13. The use of Nanotrap particles technology in capturing HIV-1 virions and viral proteins from infected cells.

    Directory of Open Access Journals (Sweden)

    Elizabeth Jaworski

    Full Text Available HIV-1 infection results in a chronic but incurable illness since long-term HAART can keep the virus to an undetectable level. However, discontinuation of therapy rapidly increases viral burden. Moreover, patients under HAART frequently develop various metabolic disorders and HIV-associated neuronal disease. Today, the main challenge of HIV-1 research is the elimination of the residual virus in infected individuals. The current HIV-1 diagnostics are largely comprised of serological and nucleic acid based technologies. Our goal is to integrate the nanotrap technology into a standard research tool that will allow sensitive detection of HIV-1 infection. This study demonstrates that majority of HIV-1 virions in culture supernatants and Tat/Nef proteins spiked in culture medium can be captured by nanotrap particles. To determine the binding affinities of different baits, we incubated target molecules with nanotrap particles at room temperature. After short sequestration, materials were either eluted or remained attached to nanotrap particles prior to analysis. The unique affinity baits of nanotrap particles preferentially bound HIV-1 materials while excluded albumin. A high level capture of Tat or Tat peptide by NT082 and NT084 particles was measured by western blot (WB. Intracellular Nef protein was captured by NT080, while membrane-associated Nef was captured by NT086 and also detected by WB. Selective capture of HIV-1 particles by NT073 and NT086 was measured by reverse transcriptase assay, while capture of infectious HIV-1 by these nanoparticles was demonstrated by functional transactivation in TZM-bl cells. We also demonstrated specific capture of HIV-1 particles and exosomes-containing TAR-RNA in patients' serum by NT086 and NT082 particles, respectively, using specific qRT-PCR. Collectively, our data indicate that certain types of nanotrap particles selectively capture specific HIV-1 molecules, and we propose to use this technology as a

  14. The Use of Nanotrap Particles Technology in Capturing HIV-1 Virions and Viral Proteins from Infected Cells

    Science.gov (United States)

    Sampey, Gavin; Shafagati, Nazly; Van Duyne, Rachel; Iordanskiy, Sergey; Kehn-Hall, Kylene; Liotta, Lance; Petricoin, Emanuel; Young, Mary; Lepene, Benjamin; Kashanchi, Fatah

    2014-01-01

    HIV-1 infection results in a chronic but incurable illness since long-term HAART can keep the virus to an undetectable level. However, discontinuation of therapy rapidly increases viral burden. Moreover, patients under HAART frequently develop various metabolic disorders and HIV-associated neuronal disease. Today, the main challenge of HIV-1 research is the elimination of the residual virus in infected individuals. The current HIV-1 diagnostics are largely comprised of serological and nucleic acid based technologies. Our goal is to integrate the nanotrap technology into a standard research tool that will allow sensitive detection of HIV-1 infection. This study demonstrates that majority of HIV-1 virions in culture supernatants and Tat/Nef proteins spiked in culture medium can be captured by nanotrap particles. To determine the binding affinities of different baits, we incubated target molecules with nanotrap particles at room temperature. After short sequestration, materials were either eluted or remained attached to nanotrap particles prior to analysis. The unique affinity baits of nanotrap particles preferentially bound HIV-1 materials while excluded albumin. A high level capture of Tat or Tat peptide by NT082 and NT084 particles was measured by western blot (WB). Intracellular Nef protein was captured by NT080, while membrane-associated Nef was captured by NT086 and also detected by WB. Selective capture of HIV-1 particles by NT073 and NT086 was measured by reverse transcriptase assay, while capture of infectious HIV-1 by these nanoparticles was demonstrated by functional transactivation in TZM-bl cells. We also demonstrated specific capture of HIV-1 particles and exosomes-containing TAR-RNA in patients' serum by NT086 and NT082 particles, respectively, using specific qRT-PCR. Collectively, our data indicate that certain types of nanotrap particles selectively capture specific HIV-1 molecules, and we propose to use this technology as a platform to enhance HIV-1

  15. APM_GUI: analyzing particle movement on the cell membrane and determining confinement

    Directory of Open Access Journals (Sweden)

    Menchón Silvia A

    2012-02-01

    Full Text Available Abstract Background Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,. Results Here, we present APM_GUI (Analyzing Particle Movement, which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with. Conclusions APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.

  16. Heterotrophic free-living and particle-bound bacterial cell size in the river Cauvery and its downstream tributaries

    Indian Academy of Sciences (India)

    T S Harsha; Sadanand M Yamakanamardi; M Mahadevaswamy

    2007-03-01

    This is the first comprehensive study on planktonic heterotrophic bacterial cell size in the river Cauvery and its important tributaries in Karnataka State, India. The initial hypothesis that the mean cell size of planktonic heterotrophic bacteria in the four tributaries are markedly different from each other and also from that in the main river Cauvery was rejected, because all five watercourses showed similar planktonic heterotrophic bacterial cell size. Examination of the correlation between mean heterotrophic bacterial cell size and environmental variables showed four correlations in the river Arkavathy and two in the river Shimsha. Regression analysis revealed that 18% of the variation in mean heterotrophic free-living bacterial cell size was due to biological oxygen demand (BOD) in the river Arkavathy, 11% due to surface water velocity (SWV) in the river Cauvery and 11% due to temperature in the river Kapila. Heterotrophic particle-bound bacterial cell size variation was 28% due to chloride and BOD in the river Arkavathy, 11% due to conductivity in the river Kapila and 8% due to calcium in the river Cauvery. This type of relationship between heterotrophic bacterial cell size and environmental variables suggests that, though the mean heterotrophic bacterial cell size was similar in all the five water courses, different sets of environmental variables apparently control the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible cause for this environmental (bottom–up) control is discussed.

  17. Simulation of Deformation and Aggregation of Two Red Blood Cells in a Stenosed Microvessel by Dissipative Particle Dynamics.

    Science.gov (United States)

    Xiao, Lanlan; Liu, Yang; Chen, Shuo; Fu, Bingmei

    2016-12-01

    The motion of two red blood cells in a stenosed microvessel was simulated using dissipative particle dynamics. The effects of intercellular interaction, red blood cell deformability and the initial cell orientation on the deformation and aggregation of the RBCs and on the flow resistance were investigated. The red blood cell membrane was treated as a three-dimensional coarse-grained network model and the intercellular interaction was modeled by the Morse potential based on a depletion-mediated assumption. It is shown that the flow resistance increases dramatically when the red blood cells enter into the stenosis and decreases rapidly as RBCs move away from the stenosis. Particularly, for a pair of stiffer red blood cells with the initial inclination angle of 90°, the maximum value of the flow resistance is larger; while a higher flow resistance can also come from a stronger aggregation. For a pair of stiffer red blood cells moving parallel to the main flow, when their positions are closer to the vessel wall at the upstream of the stenosis, the flow resistance increases due to the migration to the vessel center at the stenosis. In addition, for a pair of red blood cells with the initial inclination angle of 0°, the flow resistance from the aggregate formed by a pair of red blood cells with a larger deformation is higher.

  18. Fabrication of substrates with curvature for cell cultivation by alpha-particle irradiation and chemical etching of PADC films

    Energy Technology Data Exchange (ETDEWEB)

    Ng, C.K.M.; Tjhin, V.T. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong (Hong Kong); Lin, A.C.C.; Cheng, J.P.; Cheng, S.H. [Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong (Hong Kong); Yu, K.N., E-mail: peter.yu@cityu.edu.hk [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong (Hong Kong)

    2012-05-01

    In the present paper, we developed a microfabrication technology to generate cell-culture substrates with identical chemistry and well-defined curvature. Micrometer-sized pits with curved surfaces were created on a two-dimensional surface of a polymer known as polyallyldiglycol carbonate (PADC). A PADC film was first irradiated by alpha particles and then chemically etched under specific conditions to generate pits with well-defined curvature at the incident positions of the alpha particles. The surface with these pits was employed as a model system for studying the effects of substrate curvature on cell behavior. As an application, the present work studied mechanosensing of substrate curvature by epithelial cells (HeLa cells) through regulation of microtubule (MT) dynamics. We used end-binding protein 3-green fluorescent protein (EB3-GFP) as a marker of MT growth to show that epithelial cells having migrated into the pits with curved surfaces had significantly smaller MT growth speeds than those having stayed on flat surfaces without the pits.

  19. Particle dynamics and effective temperature of jammed granular matter in a slowly sheared three-dimensional Couette cell.

    Science.gov (United States)

    Wang, Ping; Song, Chaoming; Briscoe, Christopher; Makse, Hernán A

    2008-06-01

    We report experimental measurements of particle dynamics on slowly sheared granular matter in a three-dimensional Couette cell. A closely packed ensemble of transparent spherical beads is confined by an external pressure and filled with fluid to match both the density and refractive index of the beads. This allows us to track tracer particles embedded in the system and obtain three-dimensional trajectories [r(t),theta(t),z(t)] as a function of time. We study the probability distribution function of the vertical and radial displacements, finding Gaussian and exponential distributions, respectively. For slow shear rates, the mean-square fluctuations in all three directions are found to be dependent only on the angular displacement of the Couette cell, Delta theta e, (Delta z 2) approximately Delta theta e, (Delta r2) approximately Delta theta e alpha, Delta theta 2 approximately Delta theta e beta, where alpha and beta are constants. With Delta theta e proportional to the time between measurements, the values of the constants, alpha and beta , are found to be subdiffusive and superdiffusive, respectively. ThFe linear relation between (Delta z 2) and angular displacement implies a diffusive process, from which we can calculate an "effective temperature," T eff, in the vertical direction, through a fluctuation-dissipation relation. It is of interest to determine whether these systems can be described by analogous equilibrium statistical mechanics concepts such as "effective temperature" and "compactivity." By studying the dynamics of tracer particles, we find the effective temperature defined by the Stokes-Einstein relation to be independent of the tracer particle characteristic features, such as density and size, and dependent only on the packing density of the system. For slow shear rate, both the diffusivity and mobility of tracer particles are proportional to the shear rate, giving rise to a constant effective temperature, characteristic of the jammed system. We

  20. Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics.

    Science.gov (United States)

    Sevink, G J A; Schmid, F; Kawakatsu, T; Milano, G

    2017-02-22

    We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion. Since collisions are seriously affected by the softening of non-bonded interactions that originates from their evaluation at the coarser continuum level, we have devised a way to reinsert the effect of collisions on the structural evolution. Merging MD-SCF with multi-particle collision dynamics (MPCD), we mimic particle collisions at the level of computational cells and at the same time properly account for the momentum transfer that is important for a realistic system evolution. The resulting hybrid MD-SCF/MPCD method was validated for a particular coarse-grained model of phospholipids in aqueous solution, against reference full-particle simulations and the original MD-SCF model. We additionally implemented and tested an alternative and more isotropic finite difference gradient. Our results show that efficiency is improved by merging MD-SCF with MPCD, as properly accounting for hydrodynamic interactions considerably speeds up the phase separation dynamics, with negligible additional computational costs compared to efficient MD-SCF. This new method enables realistic simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

  1. ONCOGENIC TRANSFORMATION OF SYRIAN HAMSTER EMBRYO CELLS BY 5.3-MeVα PARTICLES AND A TUMOR PROMOTER PHORBOL ESTER

    Institute of Scientific and Technical Information of China (English)

    寿江; 龚诒芬; 吴德昌

    1996-01-01

    The primary Syrian hamster embryo(SHE) cells were used to study the oneogenic transformation by 235pu a particles or X-rays alone or in combination with a chemical promoter phorbol ester. Survival curves of SHE cells following exposure to a-partieles or X-rays were fitted to single-or multi-target models,respectively. Model parameters were:Do=0. 55 Gy,n= 1 for a particles;Do=l. 44 Gy,Dq 3. 0 Gy,n=7. 7 for X-rays. Incidence of a particles or X-rays induced cell transformation was dose-dependant, a partieles were more efficient in inducing cell transformation than that of X rays. The enhancement of SHE cell transformarion by phorbol 12-myristate 13-acetate(PMA) following exposure to a particles of 0. 25-1.00 Gy was observed.

  2. Polyubiquitinated proteins, proteasome, and glycogen characterize the particle-rich cytoplasmic structure (PaCS) of neoplastic and fetal cells.

    Science.gov (United States)

    Necchi, Vittorio; Sommi, Patrizia; Vitali, Agostina; Vanoli, Alessandro; Savoia, Anna; Ricci, Vittorio; Solcia, Enrico

    2014-05-01

    A particle-rich cytoplasmic structure (PaCS) concentrating ubiquitin-proteasome system (UPS) components and barrel-like particles in clear, cytoskeleton- and organelle-free areas has recently been described in some neoplasms and in genetic or infectious diseases at risk of neoplasia. Ultrastructurally similar particulate cytoplasmic structures, interpreted as glycogen deposits, have previously been reported in clear-cell neoplasms and some fetal tissues. It remains to be investigated whether the two structures are the same, colocalize UPS components and polysaccharides, and have a role in highly proliferative cells such as fetal and neoplastic cells. We used immunogold electron microscopy and confocal immunofluorescence microscopy to examine human and mouse fetal tissues and human neoplasms. Fetal and neoplastic cells both showed colocalization of polyubiquitinated proteins, 19S and 20S proteasomes, and polysaccharides, both glycogen and chondroitin sulfate, inside cytoplasmic structures showing all distinctive features of PaCSs. Poorly demarcated and/or hybrid (ribosomes admixed) UPS- and glycogen-enriched areas, likely stages in PaCS development, were also seen in some fetal cells, with special reference to those, like primary alveolar pulmonary cells or pancreatic centroacinar cells, having a crucial role in organogenesis. UPS- and glycogen-rich PaCSs developed extensively in clear-cell neoplasms of the kidney, ovary, pancreas, and other organs, as well as, in infantile, development-related tumors replicating fetal patterns, such as choroid plexus papilloma. UPS-mediated, ATP-dependent proteolysis and its potential energy source, glycogen metabolism, may have a crucial, synergic role in embryo-/organogenesis and carcinogenesis.

  3. Generation of hydrogen peroxide from San Joaquin Valley particles in a cell-free solution

    Directory of Open Access Journals (Sweden)

    H. Shen

    2010-09-01

    Full Text Available Epidemiological studies have shown a correlation between exposure to ambient particulate matter (PM and adverse health effects. One proposed mechanism of PM-mediated health effects is the generation of reactive oxygen species (ROS – e.g., superoxide (•O2, hydrogen peroxide (HOOH, and hydroxyl radical (•OH – followed by oxidative stress. There are very few quantitative, specific measures of individual ROS generated from PM, but this information would help to more quantitatively address the link between ROS and the health effects of PM. To address this gap, we quantified the generation of HOOH by PM collected at an urban (Fresno and rural (Westside site in the San Joaquin Valley (SJV of California during summer and winter from 2006 to 2009. HOOH was quantified by HPLC after extracting the PM in a cell-free, phosphate-buffered saline (PBS solution with or without 50 μM ascorbate (Asc. Our results show that the urban PM generally generates much more HOOH than the rural PM but that there is no apparent seasonal difference in HOOH generation. In nearly all of the samples the addition of a physiologically relevant concentration of Asc greatly enhances HOOH formation, but a few of the coarse PM samples were able to generate a considerable amount of HOOH in the absence of added Asc, indicating the presence of unknown reductants. Normalized by air volume, the fine PM (PM2.5 generally makes more HOOH than the corresponding coarse PM (PMcf, i.e., 2.5 to 10 μm, primarily because the mass concentration of PM2.5 is much higher than that of PMcf. However, normalized by PM mass, the coarse PM typically generates more HOOH than the fine PM. The amount of HOOH produced by SJV PM is reduced on average by (78±15% when the transition metal chelator desferoxamine (DSF is added to the extraction solution, indicating that transition metals play a dominant role in HOOH generation. By

  4. Generation of hydrogen peroxide from San Joaquin Valley particles in a cell-free solution

    Directory of Open Access Journals (Sweden)

    H. Shen

    2011-01-01

    Full Text Available Epidemiological studies have shown a correlation between exposure to ambient particulate matter (PM and adverse health effects. One proposed mechanism of PM-mediated health effects is the generation of reactive oxygen species (ROS – e.g., superoxide (O2, hydrogen peroxide (HOOH, and hydroxyl radical (OH – followed by oxidative stress. There are very few quantitative, specific measures of individual ROS generated from PM, but this information would help to more quantitatively address the link between ROS and the health effects of PM. To address this gap, we quantified the generation of HOOH by PM collected at an urban (Fresno and rural (Westside site in the San Joaquin Valley (SJV of California during summer and winter from 2006 to 2009. HOOH was quantified by HPLC after extracting the PM in a cell-free, phosphate-buffered saline (PBS solution with or without 50 μM ascorbate (Asc. Our results show that the urban PM generally generates much more HOOH than the rural PM but that there is no apparent seasonal difference in HOOH generation. In nearly all of the samples the addition of a physiologically relevant concentration of Asc greatly enhances HOOH formation, but a few of the coarse PM samples were able to generate a considerable amount of HOOH in the absence of added Asc, indicating the presence of unknown reductants. Normalized by air volume, the fine PM (PM2.5 generally makes more HOOH than the corresponding coarse PM (PMcf, i.e., 2.5 to 10 μm, primarily because the mass concentration of PM2.5 is much higher than that of PMcf. However, normalized by PM mass, the coarse PM typically generates more HOOH than the fine PM. The amount of HOOH produced by SJV PM is reduced on average by (78 ± 15% when the transition metal chelator desferoxamine (DSF is added to the extraction solution, indicating that transition metals play a dominant role in HOOH

  5. Particle-based transcutaneous administration of HIV-1 p24 protein to human skin explants and targeting of epidermal antigen presenting cells.

    Science.gov (United States)

    Rancan, Fiorenza; Amselgruber, Sarah; Hadam, Sabrina; Munier, Sevérine; Pavot, Vincent; Verrier, Bernard; Hackbarth, Steffen; Combadiere, Behazine; Blume-Peytavi, Ulrike; Vogt, Annika

    2014-02-28

    Transcutaneous immunization is a promising vaccination strategy for the treatment of infectious diseases and cancer. In this study, we investigate the combination of cyanoacrylate skin surface stripping (CSSS) and particle-based antigen delivery to target the HIV-1 p24 protein to skin antigen presenting cells (APC). The CSSS treatment pre-activates skin APC and opens hair follicles, where protein-loaded particles accumulate and allow for sustained delivery of the loaded antigen to perifollicular APC. We found that poly-lactic acid (PLA) and polystyrene (PS) particles targeted the adsorbed HIV-1 p24 protein to the hair follicles. Small amounts of PS and PLA particles were found to translocate to the epidermis and be internalized by skin cells, whereas most of the particles aggregated in the hair follicle canal, where they released the loaded antigen. The p24 protein diffused to the epidermis and dermis and was detected in skin cells, especially in Langerhans cells and dermal dendritic cells. Furthermore, the combination of CSSS and particle-based delivery resulted in activation and maturation of Langerhans cells (HLA-DR, CD80 and CD83). We conclude that particle-based antigen delivery across partially disrupted skin barrier is a feasible and effective approach to needle-free transcutaneous vaccination.

  6. Enrichment of Fetal Nucleated Red Blood Cells by Multi-core Magnetic Composite Particles for Non-invasive Prenatal Diagnosis

    Institute of Scientific and Technical Information of China (English)

    PAN Ying; ZHANG Ai-chen; WANG Qing; HUANG Wen-jun; QIAO Feng-li; LIU Yu-ping; ZHANG Yu-cheng; HAl De-yang; DU Ying-ting; WANG Wen-yue

    2012-01-01

    A novel kind of multi-core magnetic composite particles,the surfaces of which were respectively modified with goat-anti-mouse IgG and antitransferrin receptor(anti-CD71 ),was prepared.The fetal nucleated red blood cells(FNRBCs) in the peripheral blood of a gravida were rapidly and effectively enriched and separated by the modified multi-core magnetic composite particles in an external magnetic field.The obtained FNRBCs were used for the identification of the fetal sex by means of fluorescence in situ hybridization(FISH) technique.The results demonstrate that the multi-core magnetic composite particles meet the requirements for the enrichment and speration of FNRBCs with a low concentration and the accuracy of detetion for the diagnosis of fetal sex reached to 95%.Moreover,the obtained FNRBCs were applied to the non-invasive diagnosis of Down syndrome and chromosome 3p21 was detected.The above facts indicate that the novel multi-core magnetic composite particles-based method is simple,reliable and cost-effective and has opened up vast vistas for the potential application in clinic non-invasive prenatal diagnosis.

  7. Hybrid smoothed dissipative particle dynamics and immersed boundary method for simulation of red blood cells in flows.

    Science.gov (United States)

    Ye, Ting; Phan-Thien, Nhan; Lim, Chwee Teck; Peng, Lina; Shi, Huixin

    2017-06-01

    In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. The smoothed dissipative particle dynamics (SDPD), a particle-based method, is one of the easy and flexible methods to model such complex structure fluids. It couples the best features of the smoothed particle hydrodynamics (SPH) and dissipative particle dynamics (DPD), with parameters having specific physical meaning (coming from SPH discretization of the Navier-Stokes equations), combined with thermal fluctuations in a mesoscale simulation, in a similar manner to the DPD. On the other hand, the immersed boundary method (IBM), a preferred method for handling fluid-structure interaction problems, has also been widely used to handle the fluid-RBC interaction in RBC simulations. In this paper, we aim to couple SDPD and IBM together to carry out the simulations of RBCs in complex flow problems. First, we develop the SDPD-IBM model in details, including the SDPD model for the evolving fluid flow, the RBC model for calculating RBC deformation force, the IBM for treating fluid-RBC interaction, and the solid boundary treatment model as well. We then conduct the verification and validation of the combined SDPD-IBM method. Finally, we demonstrate the capability of the SDPD-IBM method by simulating the flows of RBCs in rectangular, cylinder, curved, bifurcated, and constricted tubes, respectively.

  8. Effects of variations in electron thermal velocity on the whistler anisotropy instability: Particle-in-cell simulations

    Science.gov (United States)

    Hughes, R. Scott; Wang, Joseph; Decyk, Viktor K.; Gary, S. Peter

    2016-04-01

    This paper investigates how the physics of the whistler anisotropy instability (WAI) is affected by variations in the electron thermal velocity vte, referred to here in terms of the ratio v̂ t e=vt e/c , where c is the speed of light. The WAI is driven by the electron condition RT>1 , where RT=Te ⊥/Te ∥ is the temperature anisotropy ratio and ⊥/∥ signify directions perpendicular/parallel to the background magnetic field B0 . While a typical value of v̂ t e in the solar wind is ˜0.005 , electromagnetic (EM) particle-in-cell (PIC) simulations often use a value near 0.1 in order to maximize the computational time step. In this study, a two-dimensional (2D) Darwin particle-in-cell (DPIC) code, MDPIC2, is used. The time step in the DPIC model is not affected by the choice of v̂ t e , making DPIC suited for this study. A series of simulations are carried out under the condition that the electron βe is held fixed, while v̂ t e is varied over the range 0.1 ≥v̂ t e≥0.025 . The results show that, with βe held fixed, the linear dispersion properties and the nonlinear saturation amplitude and pitch angle scattering rates associated with the WAI are insensitive to the value of v̂ t e . A supplementary investigation is conducted which characterizes how the WAI model is affected at various values of v̂ t e by noise associated with the limited number of particles in a typical PIC simulation. It is found that the evolution of the WAI is more strongly influenced by electrostatic noise as v̂ t e is decreased. The electrostatic noise level is inversely proportional to the number of particles per computational cell ( Nc ); this implies that the number of particles required to remove nonphysical effects from the PIC simulation increases as v̂ t e decreases. It is concluded that PIC simulations of this instability which use an artificially large value of v̂ t e accurately reproduce the response of a cooler plasma as long as a realistic value of βe is used

  9. Targeting of phage particles towards endothelial cells by antibodies selected through a multi-parameter selection strategy

    Science.gov (United States)

    Mandrup, Ole A.; Lykkemark, Simon; Kristensen, Peter

    2017-01-01

    One of the hallmarks of cancer is sustained angiogenesis. Here, normal endothelial cells are activated, and their formation of new blood vessels leads to continued tumour growth. An improved patient condition is often observed when angiogenesis is prevented or normalized through targeting of these genomically stable endothelial cells. However, intracellular targets constitute a challenge in therapy, as the agents modulating these targets have to be delivered and internalized specifically to the endothelial cells. Selection of antibodies binding specifically to certain cell types is well established. It is nonetheless a challenge to ensure that the binding of antibodies to the target cell will mediate internalization. Previously selection of such antibodies has been performed targeting cancer cell lines; most often using either monovalent display or polyvalent display. In this article, we describe selections that isolate internalizing antibodies by sequential combining monovalent and polyvalent display using two types of helper phages, one which increases display valence and one which reduces background. One of the selected antibodies was found to mediate internalization into human endothelial cells, although our results confirms that the single stranded nature of the DNA packaged into phage particles may limit applications aimed at targeting nucleic acids in mammalian cells. PMID:28186116

  10. Impact of the composition of combustion generated fine particles on epithelial cell toxicity: influences of metals on metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Okeson, C.D.; Riley, M.R.; Fernandez, A.; Wendt, J.O.L. [University of Arizona, Tucson, AZ (USA). Dept. of Agriculture & Biosystems Engineering

    2003-06-01

    Inhaled airborne particulate matter (PM) represents a potentially significant health hazard to humans. PM generated from the combustion of fuel oils and coals contain a number of water-soluble transition metals including Fe, V, and Zn. The authors evaluated the impact of PM types with varying composition collected from the combustion of oils and coals on the health and metabolism of lung cell cultures. Three colorimetric assays (sulforhodamine B (SRB), Janus green, and MTT) were adapted to quantify the impact of PM on rat lung alveolar type 11 epithelial cells (RLE-6TN cells). The PM toxicity metrics evaluated were inhibition of cell proliferation (SRB and Janus green) and inhibition of cellular metabolism (MTT). Cell proliferation is inhibited in a consistent dose-dependent manner by PM concentrations from 25 to 250 {mu}g/ml. At a level of 100 {mu}g/ml, oil-derived PM diminishes cell metabolism by as much as 40% relative to controls; the degree of inhibition is strongly dependent on PM particle size and metal content. Conversely, coal-derived PM at the same dosage diminishes cell metabolism by no more than 20% relative to controls. All three assays provide highly repeatable results and consistent toxicity rankings of the PMs evaluated. Overall, metabolic inhibition as measured by the MTT assay was deemed the most appropriate metric for PM toxicity, primarily due to its applicability with in vivo-like confluent cell monolayers.

  11. Lorentz boosted frame simulation technique in Particle-in-cell methods

    Science.gov (United States)

    Yu, Peicheng

    In this dissertation, we systematically explore the use of a simulation method for modeling laser wakefield acceleration (LWFA) using the particle-in-cell (PIC) method, called the Lorentz boosted frame technique. In the lab frame the plasma length is typically four orders of magnitude larger than the laser pulse length. Using this technique, simulations are performed in a Lorentz boosted frame in which the plasma length, which is Lorentz contracted, and the laser length, which is Lorentz expanded, are now comparable. This technique has the potential to reduce the computational needs of a LWFA simulation by more than four orders of magnitude, and is useful if there is no or negligible reflection of the laser in the lab frame. To realize the potential of Lorentz boosted frame simulations for LWFA, the first obstacle to overcome is a robust and violent numerical instability, called the Numerical Cerenkov Instability (NCI), that leads to unphysical energy exchange between relativistically drifting particles and their radiation. This leads to unphysical noise that dwarfs the real physical processes. In this dissertation, we first present a theoretical analysis of this instability, and show that the NCI comes from the unphysical coupling of the electromagnetic (EM) modes and Langmuir modes (both main and aliasing) of the relativistically drifting plasma. We then discuss the methods to eliminate them. However, the use of FFTs can lead to parallel scalability issues when there are many more cells along the drifting direction than in the transverse direction(s). We then describe an algorithm that has the potential to address this issue by using a higher order finite difference operator for the derivative in the plasma drifting direction, while using the standard second order operators in the transverse direction(s). The NCI for this algorithm is analyzed, and it is shown that the NCI can be eliminated using the same strategies that were used for the hybrid FFT

  12. Residual baculovirus in insect cell-derived influenza virus-like particle preparations enhances immunogenicity.

    Directory of Open Access Journals (Sweden)

    Irina Margine

    Full Text Available Influenza virus-like particles are currently evaluated in clinical trials as vaccine candidates for influenza viruses. Most commonly they are produced in baculovirus- or mammalian- expression systems. Here we used different vaccination schemes in order to systematically compare virus-like particle preparations generated in the two systems. Our work shows significant differences in immunogenicity between the two, and indicates superior and broader immune responses induced by the baculovirus-derived constructs. We demonstrate that these differences critically influence protection and survival in a mouse model of influenza virus infection. Finally, we show that the enhanced immunogenicity of the baculovirus-derived virus-like particles is caused by contamination with residual baculovirus which activates the innate immune response at the site of inoculation.

  13. Application of a Halbach magnetic array for long-range cell and particle separations in biological samples

    Science.gov (United States)

    Kang, Joo H.; Driscoll, Harry; Super, Michael; Ingber, Donald E.

    2016-05-01

    Here, we describe a versatile application of a planar Halbach permanent magnet array for an efficient long-range magnetic separation of living cells and microparticles over distances up to 30 mm. A Halbach array was constructed from rectangular bar magnets using 3D-printed holders and compared to a conventional alternating array of identical magnets. We theoretically predicted the superiority of the Halbach array for a long-range magnetic separation and then experimentally validated that the Halbach configuration outperforms the alternating array for isolating magnetic microparticles or microparticle-bound bacterial cells at longer distances. Magnetophoretic velocities (ymag) of magnetic particles (7.9 μm diameter) induced by the Halbach array in a microfluidic device were significantly higher and extended over a larger area than those induced by the alternating magnet array (ymag = 178 versus 0 μm/s at 10 mm, respectively). When applied to 50 ml tubes (˜30 mm diameter), the Halbach array removed >95% of Staphylococcus aureus bacterial cells bound with 1 μm magnetic particles compared to ˜70% removed using the alternating array. In addition, the Halbach array enabled manipulation of 1 μm magnetic beads in a deep 96-well plate for ELISA applications, which was not possible with the conventional magnet arrays. Our analysis demonstrates the utility of the Halbach array for the future design of devices for high-throughput magnetic separations of cells, molecules, and toxins.

  14. Effects of the disaggregation of high-polymerized particles in guard cell vacuoles on osmoregulation of stomatal aperture (stomata opening)

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Observation under an electron microscope reveals that in closed and open stomata of V. faba, the average volume of particles in guard cell vacuoles (GCV) reduces about 3 orders in magnitude, while the distribution density of the particles increases about 2 orders of magnitude. By using the method of the ratio of fluorescent emissions with laser scanning confocal microscopy, the monitoring to stomata opening shows that during 10 to 30 s before the first distinguishable aperture of stomata, there is a change of pH in GCV about-0.5 units. A quick stomatal opening immediately follows the changes of pH in GCV to reach a steady aperture about 12μm in 100-200 s. This work proposes a model for the osmoregulation in GCV for stomatal opening. The proposed osmoregulation is related to the disaggregation of some polymerized particles inside GCV, which is probably induced by a -(pH in the vacuole. This model describes a process of osmoregulation that avoids the massive energy consuming transportation across cell membranes, which is a foundation of the current chemiosmotic hypothesis. This model is a supplement to the multiple controlling hypothesis for the stomatal movement, which widens research principle ideas for other quick movements in plants.

  15. Simulation study of dose enhancement in a cell due to nearby carbon and oxygen in particle radiotherapy

    CERN Document Server

    Shin, Jae Ik; Cho, Sungho; Kim, Eun Ho; Song, Yongkeun; Jung, Won-Gyun; Yoo, SeungHoon; Shin, Dongho; Lee, Se Byeong; Yoon, Myonggeun; Incerti, Sebastian; Geso, Moshi; Rosenfeld, Anatoly B

    2015-01-01

    The aim of