bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjuvant-like Effect of Vaccinia Virus 14K Protein: A Case Study with Malaria Vaccine Based on the Circumsporozoite Protein
Authors: Vijayan Aneesh , Gómez Carmen E. , Espinosa Diego A. , Goodman Alan G. , Sanchez-Sampedro Lucas , Sorzano Carlos Oscar S. , Zavala Fidel , Esteban Mariano 
Published: May 2012

Abstract
Development of subunit vaccines for malaria that elicit a strong, long-term memory response is an intensive area of research, with the focus on improving the immunogenicity of a circumsporozoite (CS) protein-based vaccine. In this study, we found that a chimeric protein, formed by fusing vaccinia virus protein 14K (A27) to the CS of Plasmodium yoelii, induces strong effector memory CD8+ T cell responses in addition to high-affinity Abs when used as a priming agent in the absence of any adjuvant, followed by an attenuated vaccinia virus boost expressing CS in murine models. Moreover, priming with the chimeric protein improved the magnitude and polyfunctionality of cytokine-secreting CD8+ T cells. This fusion protein formed oligomers/aggregates that led to activation of STAT-1 and IFN regulatory factor-3 in human macrophages, indicating a type I IFN response, resulting in NO, IL-12, and IL-6 induction. Furthermore, this vaccination regimen inhibited the liver stage development of the parasite, resulting in sterile protection. In summary, we propose a novel approach in designing CS based pre-erythrocytic vaccines against Plasmodium using the adjuvant-like effect of the immunogenic vaccinia virus protein 14K.
A Multigrid Method for a Model of the Implicit Immersed Boundary Equations
Authors: Guy Robert D. , Philip Bobby 
Published: May 2012

AbstractExplicit time stepping schemes for the immersed boundary method require very small time steps in order to maintain stability. Solving the equations that arise from an implicit discretization is difficult. Recently, several different approaches have been proposed, but a complete understanding of this problem is still emerging. A multigrid method is developed and explored for solving the equations in an implicit-time discretization of a model of the immersed boundary equations. The model problem consists of a scalar Poisson equation with conformation-dependent singular forces on an immersed boundary. This model does not include the inertial terms or the incompressibility constraint. The method is more efficient than an explicit method, but the efficiency gain is limited. The multigrid method alone may not be an effective solver, but when used as a preconditioner for Krylov methods, the speed-up over the explicit-time method is substantial. For example, depending on the constitutive law for the boundary force, with a time step 100 times larger than the explicit method, the implicit method is about 15-100 times more efficient than the explicit method. A very attractive feature of this method is that the efficiency of the multigrid preconditioned Krylov solver is shown to be independent of the number of immersed boundary points.
Power Laws and Skew Distributions
Authors: Mahnke Reinhard , Kaupužs Jevgenijs , Brics Mārtiņš 
Published: May 2012

AbstractPower-law distributions and other skew distributions, observed in various models and real systems, are considered. A model, describing evolving systems with increasing number of elements, is considered to study the distribution over element sizes. Stationary power-law distributions are found. Certain non-stationary skew distributions are obtained and analyzed, based on exact solutions and numerical simulations.
A Unified Gas-Kinetic Scheme for Continuum and Rarefied Flows II: Multi-Dimensional Cases
Authors: Huang Juan-Chen , Xu Kun , Yu Pubing 
Published: May 2012

AbstractWith discretized particle velocity space, a multi-scale unified gas-kinetic scheme for entire Knudsen number flows has been constructed based on the kinetic model in one-dimensional case [J. Comput. Phys., vol. 229 (2010), pp. 7747-7764]. For the kinetic equation, to extend a one-dimensional scheme to multidimensional flow is not so straightforward. The major factor is that addition of one dimension in physical space causes the distribution function to become two-dimensional, rather than axially symmetric, in velocity space. In this paper, a unified gas-kinetic scheme based on the Shakhov model in two-dimensional space will be presented. Instead of particle-based modeling for the rarefied flow, such as the direct simulation Monte Carlo (DSMC) method, the philosophical principal underlying the current study is a partial-differential-equation (PDE)-based modeling. Since the valid scale of the kinetic equation and the scale of mesh size and time step may be significantly different, the gas evolution in a discretized space is modeled with the help of kinetic equation, instead of directly solving the partial differential equation. Due to the use of both hydrodynamic and kinetic scales flow physics in a gas evolution model at the cell interface, the unified scheme can basically present accurate solution in all flow regimes from the free molecule to the Navier-Stokes solutions. In comparison with the DSMC and Navier-Stokes flow solvers, the current method is much more efficient than DSMC in low speed transition and continuum flow regimes, and it has better capability than NS solver in capturing of non-equilibrium flow physics in the transition and rarefied flow regimes. As a result, the current method can be useful in the flow simulation where both continuum and rarefied flow physics needs to be resolved in a single computation. This paper will extensively evaluate the performance of the unified scheme from free molecule to continuum NS solutions, and from low speed micro-flow to high speed non-equilibrium aerodynamics. The test cases clearly demonstrate that the unified scheme is a reliable method for the rarefied flow computations, and the scheme provides an important tool in the study of non-equilibrium flow.
Numerical Regularized Moment Method For High Mach Number Flow
Authors: Cai Zhenning , Li Ruo , Wang Yanli 
Published: May 2012

AbstractThis paper is a continuation of our earlier work [SIAM J. Sci. Comput., 32(2010), pp. 2875-2907] in which a numerical moment method with arbitrary order of moments was presented. However, the computation may break down during the calculation of the structure of a shock wave with Mach number M0≥ 3. In this paper, we concentrate on the regularization of the moment systems. First, we apply the Maxwell iteration to the infinite moment system and determine the magnitude of each moment with respect to the Knudsen number. After that, we obtain the approximation of high order moments and close the moment systems by dropping some high-order terms. Linearization is then performed to obtain a very simple regularization term, thus it is very convenient for numerical implementation. To validate the new regularization, the shock structures of low order systems are computed with different shock Mach numbers.
Extension Of The High-Order Space-Time Discontinuous Galerkin Cell Vertex Scheme To Solve Time Dependent Diffusion Equations
Authors: Tu Shuangzhang , Skelton Gordon W. , Pang Qing 
Published: May 2012

AbstractIn this paper, the high-order space-time discontinuous Galerkin cell vertex scheme (DG-CVS) developed by the authors for hyperbolic conservation laws is extended for time dependent diffusion equations. In the extension, the treatment of the diffusive flux is exactly the same as that for the advective flux. Thanks to the Riemann-solver-free and reconstruction-free features of DG-CVS, both the advective flux and the diffusive flux are evaluated using continuous information across the cell interface. As a result, the resulting formulation with diffusive fluxes present is still consistent and does not need any extra ad hoc techniques to cure the common “variational crime” problem when traditional DG methods are applied to diffusion problems. For this reason, DG-CVS is conceptually simpler than other existing DG-typed methods.
A Parallel Domain Decomposition Algorithm for Simulating Blood Flow with Incompressible Navier-Stokes Equations with Resistive Boundary Condition
Authors: Wu Yuqi , Cai Xiao-Chuan 
Published: May 2012

AbstractWe introduce and study a parallel domain decomposition algorithm for the simulation of blood flow in compliant arteries using a fully-coupled system of nonlinear partial differential equations consisting of a linear elasticity equation and the incompressible Navier-Stokes equations with a resistive outflow boundary condition. The system is discretized with a finite element method on unstructured moving meshes and solved by a Newton-Krylov algorithm preconditioned with an overlapping restricted additive Schwarz method. The resistive outflow boundary condition plays an interesting role in the accuracy of the blood flow simulation and we provide a numerical comparison of its accuracy with the standard pressure type boundary condition. We also discuss the parallel performance of the implicit domain decomposition method for solving the fully coupled nonlinear system on a supercomputer with a few hundred processors.
An Adaptive Mesh Refinement Strategy for Immersed Boundary/Interface Methods
Authors: Li Zhilin , Song Peng 
Published: May 2012

AbstractAn adaptive mesh refinement strategy is proposed in this paper for the Immersed Boundary and Immersed Interface methods for two-dimensional elliptic interface problems involving singular sources. The interface is represented by the zero level set of a Lipschitz function ϕ(x,y). Our adaptive mesh refinement is done within a small tube of |ϕ(x,y)|≤δ with finer Cartesian meshes. The discrete linear system of equations is solved by a multigrid solver. The AMR methods could obtain solutions with accuracy that is similar to those on a uniform fine grid by distributing the mesh more economically, therefore, reduce the size of the linear system of the equations. Numerical examples presented show the efficiency of the grid refinement strategy.
Aerodynamic Analysis of a Localized Flexible Airfoil at Low Reynolds Numbers
Authors: Kang Wei , Zhang Jia-Zhong , Feng Pei-Hua 
Published: May 2012

AbstractA localized flexible airfoil at low Reynolds numbers is modeled and the aerodynamic performance is analyzed numerically. With characteristic based split scheme, a fluid solver for two dimensional incompressible Navier-Stokes equations is developed under the ALE framework, coupled with the theory of shallow arch, which is approximated by Galerkin method. Further, the interactions between the unsteady flow and the shallow arch are studied in detail. In particular, the effect of the self-excited vibration of the structure on aerodynamic performance of the airfoil is investigated deeply at various angles of attack. The results show that the lift-to-drag ratio has been increased greatly compared with the rigid airfoil. Finally, the relationship between the self-excited vibration and the evolution of the flow is analyzed using FFT tools.
How the Antimicrobial Peptides Kill Bacteria: Computational Physics Insights
Authors: Chen Licui , Gao Lianghui , Fang Weihai , Golubovic Leonardo 
Published: May 2012

AbstractIn the present article, coarse grained Dissipative Particle Dynamics simulation with implementation of electrostatic interactions is developed in constant pressure and surface tension ensemble to elucidate how the antimicrobial peptide molecules affect bilayer cell membrane structure and kill bacteria. We find that peptides with different chemical-physical properties exhibit different membrane obstructing mechanisms. Peptide molecules can destroy vital functions of the affected bacteria by translocating across their membranes via worm-holes, or by associating with membrane lipids to form hydrophilic cores trapped inside the hydrophobic domain of the membranes. In the latter model, the affected membranes are strongly buckled, in accord with very recent experimental observations [G. E. Fantner et al., Nat. Nanotech., 5 (2010), pp. 280-285].
Parallel Algorithms and Software for Nuclear, Energy, and Environmental Applications. Part II: Multiphysics Software
Authors: Gaston Derek , Guo Luanjing , Hansen Glen , Huang Hai , Johnson Richard , Knoll Dana , Newman Chris , Kae Park Hyeong , Podgorney Robert , Tonks Michael , Williamson Richard 
Published: May 2012

AbstractThis paper is the second part of a two part sequence on multiphysics algorithms and software. The first [1] focused on the algorithms; this part treats the multiphysics software framework and applications based on it. Tight coupling is typically designed into the analysis application at inception, as such an application is strongly tied to a composite nonlinear solver that arrives at the final solution by treating all equations simultaneously. The application must also take care to minimize both time and space error between the physics, particularly if more than one mesh representation is needed in the solution process. This paper presents an application framework that was specifically designed to support tightly coupled multiphysics analysis. The Multiphysics Object Oriented Simulation Environment (MOOSE) is based on the Jacobian-free Newton-Krylov (JFNK) method combined with physics-based preconditioning to provide the underlying mathematical structure for applications. The report concludes with the presentation of a host of nuclear, energy and environmental applications that demonstrate the efficacy of the approach and the utility of a well-designed multiphysics framework.
High-Order and High Accurate CFD Methods and Their Applications for Complex Grid Problems
Authors: Deng Xiaogang , Mao Meiliang , Tu Guohua , Zhang Hanxin , Zhang Yifeng 
Published: May 2012

AbstractThe purpose of this article is to summarize our recent progress in high-order and high accurate CFD methods for flow problems with complex grids as well as to discuss the engineering prospects in using these methods. Despite the rapid development of high-order algorithms in CFD, the applications of high-order and high accurate methods on complex configurations are still limited. One of the main reasons which hinder the widely applications of these methods is the complexity of grids. Many aspects which can be neglected for low-order schemes must be treated carefully for high-order ones when the configurations are complex. In order to implement high-order finite difference schemes on complex multi-block grids, the geometric conservation law and block-interface conditions are discussed. A conservative metric method is applied to calculate the grid derivatives, and a characteristic-based interface condition is employed to fulfil high-order multi-block computing. The fifth-order WCNS-E-5 proposed by Deng is applied to simulate flows with complex grids, including a double-delta wing, a transonic airplane configuration, and a hypersonic X-38 configuration. The results in this paper and the references show pleasant prospects in engineering-oriented applications of high-order schemes.
On the Volume Conservation of the Immersed Boundary Method
Authors: Griffith Boyce E. 
Published: May 2012

AbstractThe immersed boundary (IB) method is an approach to problems of fluid-structure interaction in which an elastic structure is immersed in a viscous incompressible fluid. The IB formulation of such problems uses a Lagrangian description of the structure and an Eulerian description of the fluid. It is well known that some versions of the IB method can suffer from poor volume conservation. Methods have been introduced to improve the volume-conservation properties of the IB method, but they either have been fairly specialized, or have used complex, nonstandard Eulerian finite-difference discretizations. In this paper, we use quasi-static and dynamic benchmark problems to investigate the effect of the choice of Eulerian discretization on the volume-conservation properties of a formally second-order accurate IB method. We consider both collocated and staggered-grid discretization methods. For the tests considered herein, the staggered-grid IB scheme generally yields at least a modest improvement in volume conservation when compared to cell-centered methods, and in many cases considered in this work, the spurious volume changes exhibited by the staggered-grid IB method are more than an order of magnitude smaller than those of the collocated schemes. We also compare the performance of cell-centered schemes that use either exact or approximate projection methods. We find that the volume-conservation properties of approximate projection IB methods depend strongly on the formulation of the projection method. When used with the IB method, we find that pressure-free approximate projection methods can yield extremely poor volume conservation, whereas pressure-increment approximate projection methods yield volume conservation that is nearly identical to that of a cell-centered exact projection method.
Numerical Simulation of Free Surface by an Area-Preserving Level Set Method
Authors: H. Sheu Tony W. , Yu C. H. 
Published: May 2012

AbstractWe apply in this study an area preserving level set method to simulate gas/water interface flow. For the sake of accuracy, the spatial derivative terms in the equations of motion for an incompressible fluid flow are approximated by the fifth-order accurate upwinding combined compact difference (UCCD) scheme. This scheme development employs two coupled equations to calculate the first- and second-order derivative terms in the momentum equations. For accurately predicting the level set value, the interface tracking scheme is also developed to minimize phase error of the first-order derivative term shown in the pure advection equation. For the purpose of retaining the long-term accurate Hamiltonian in the advection equation for the level set function, the time derivative term is discretized by the sixth-order accurate symplectic Runge-Kutta scheme. Also, to keep as a distance function for ensuring the front having a finite thickness for all time, the re-initialization equation is used. For the verification of the optimized UCCD scheme for the pure advection equation, two benchmark problems have been chosen to investigate in this study. The level set method with excellent area conservation property proposed for capturing the interface in incompressible fluid flows is also verified by solving the dam-break, Rayleigh-Taylor instability, two-bubble rising in water, and droplet falling problems.
Stability Conditions for Wave Simulation in 3-D Anisotropic Media with the Pseudospectral Method
Authors: Zhang Wensheng 
Published: May 2012

AbstractSimulation of elastic wave propagation has important applications in many areas such as inverse problem and geophysical exploration. In this paper, stability conditions for wave simulation in 3-D anisotropic media with the pseudospectral method are investigated. They can be expressed explicitly by elasticity constants which are easy to be applied in computations. The 3-D wave simulation for two typical anisotropic media, transversely isotropic media and orthorhombic media, are carried out. The results demonstrate some satisfactory behaviors of the pseudospectral method.
SPEEDUP Code for Calculation of Transition Amplitudes via the Effective Action Approach
Authors: Balaž Antun , Vidanović Ivana , Stojiljković Danica , Vudragović Dušan , Belić Aleksandar , Bogojević Aleksandar 
Published: May 2012

AbstractWe present Path Integral Monte Carlo C code for calculation of quantum mechanical transition amplitudes for 1D models. The SPEEDUP C code is based on the use of higher-order short-time effective actions and implemented to the maximal order p=18 in the time of propagation (Monte Carlo time step), which substantially improves the convergence of discretized amplitudes to their exact continuum values. Symbolic derivation of higher-order effective actions is implemented in SPEEDUP Mathematica codes, using the recursive Schrödinger equation approach. In addition to the general 1D quantum theory, developed Mathematica codes are capable of calculating effective actions for specific models, for general 2D and 3D potentials, as well as for a general many-body theory in arbitrary number of spatial dimensions.
A Full Eulerian Fluid-Membrane Coupling Method with a Smoothed Volume-of-Fluid Approach
Authors: Ii Satoshi , Gong Xiaobo , Sugiyama Kazuyasu , Wu Jinbiao , Huang Huaxiong , Takagi Shu 
Published: May 2012

AbstractA novel full Eulerian fluid-elastic membrane coupling method on the fixed Cartesian coordinate mesh is proposed within the framework of the volume-of-fluid approach. The present method is based on a full Eulerian fluid-(bulk) structure coupling solver (Sugiyama et al., J. Comput. Phys., 230 (2011) 596-627), with the bulk structure replaced by elastic membranes. In this study, a closed membrane is consid-ered, and it is described by a volume-of-fluid or volume-fraction information generally called VOF function. A smoothed indicator (or characteristic) function is introduced as a phase indicator which results in a smoothed VOF function. This smoothed VOF function uses a smoothed delta function, and it enables a membrane singular force to be incorporated into a mixture momentum equation. In order to deal with a membrane deformation on the Eulerian mesh, a deformation tensor is introduced and updated within a compactly supported region near the interface. Both the neo-Hookean and the Skalak models are employed in the numerical simulations. A smoothed (and less dissipative) interface capturing method is employed for the advection of the VOF function and the quantities defined on the membrane. The stability restriction due to membrane stiffness is relaxed by using a quasi-implicit approach. The present method is validated by using the spherical membrane deformation problems, and is applied to a pressure-driven flow with the biconcave membrane capsules (red blood cells).
Period Multiplication in a Continuous Time Series of Radio-Frequency DBDs at Atmospheric Pressure
Authors: Zhang Jiao , Wang Yanhui , Wang Dezhen 
Published: May 2012

AbstractAs a spatially extended dissipative system with strong nonlinearity the radio-frequency (rf) dielectric-barrier discharges (DBDs) at atmospheric pressure possess complex spatiotemporal nonlinear behaviors. In this paper, the time-domain nonlinear behaviors of rf DBD in atmospheric argon are studied numerically by a one-dimensional fluid model. Simulation results show that, under appropriate controlling parameters, the rf DBD can undergo a transition from single-period state to chaos through period doubling bifurcation with increasing discharge time, i.e., the regular periodic oscillation and chaos can coexist in a long time series of the atmospheric-pressure rf DBD. With increasing applied voltage amplitude, the duration of the periodic oscillation reduces gradually and chaotic zone increases, and finally the whole discharge series becomes completely chaotic state. This is different from conventional period doubling route to chaos. Moreover, the spatial characteristics of rf period-doubling discharge and chaos, as well as the parameter range of various discharge behaviors occurring are also investigated in this paper.