Isolation and Immobilization of Influenza Virus-Specific N-SA-α-2,3-Gal Receptors Using Magnetic Nanoparticles Coated with Chitosan and Maackia amurensis Lectin

Avian influenza viruses preferentially bind to sialic acid alpha-2,3-galactose (N-SA-α-2,3-Gal) receptors on epithelial cells. Herein, we describe a procedure we have developed for isolation of N-SA-α-2,3-Gal receptors from porcine trachea using magnetic nanoparticles (NPs) coated with chitosan (NP-Ch) and functionalized with Maackia amurensis lectin (NP-lectin). Magnetic nanoparticles were coated with chitosan in a one-step co-precipitation, and then M. amurensis lectin was immobilized covalently using glutaraldehyde. Lectin coated nanoparticles were incubated with sialic acid enriched fraction of tracheal homogenate, and N-SA-α-2,3-Gal receptor was extracted under magnetic field in two cycles. The presence of 66.4 kDa protein was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The interaction of immobilized receptor (NP-Ch-R) with M. amurensis lectin (NP-Ch-R-L) was demonstrated by Fourier transform infrared spectrometry (FTIR) and thermogravimetric analysis (TGA).     

High order quadratures for the evaluation of interfacial velocities in axi-symmetric Stokes flows

We propose new high order accurate methods to compute the evolution of axi-symmetric interfacial Stokes flow. The velocity at a point on the interface is given by an integral over the surface. Quadrature rules to evaluate these integrals are developed using asymptotic expansions of the integrands, both locally about the point of evaluation, and about the poles, where the interface crosses the axis of symmetry. The local expansions yield methods that converge to the chosen order pointwise, for fixed evaluation point. The pole expansions yield corrections that remove maximal errors of low order, introduced by singular behaviour of the integrands as the evaluation point approaches the poles. An interesting example of roundoff error amplification due to cancellation is also addressed. The result is a uniformly accurate fifth order method. Second order, pointwise fifth order, and uniform fifth order methods are applied to compute three sample flows, each of which presents a different computational difficulty: an initially bar-belled drop that pinches in finite time, a drop in a strain flow that approaches a steady state, and a continuously extending drop. In each case, the fifth order methods significantly improve the ability to resolve the flow. The examples furthermore give insight into the effect of the corrections needed for uniformity. We determine conditions under which the pointwise method is sufficient to obtain resolved results, and others under which the corrections significantly improve the results.     

Towards Controlled Graft Polymerization of Poly[styrene‐co‐(maleic anhydride)] on Functionalized Silica Mediated by Oxoaminium Bromide Salt. Facile Synthetic Pathway Using Nitroxide Chemistry

A TEMPO bromide salt is used to functionalize a silica surface with nitroxyl moieties. The functionalization reaction takes place in 48 h under mild conditions. In a second step, grafts of styrene‐maleic anhydride copolymer are grown from the functionalized silica surface by heating it in the presence of the monomers. FT‐IR and TGA analysis show that the silica was first functionalized with nitroxide moieties, and then that grafts of styrene‐maleic anhydride grew from the functionalized silica surface. A reaction mechanism is proposed in order to explain the findings. The results suggest that the oxoaminium salts are good candidates for the functionalization and grafting of surfaces that contain hydroxy groups and for the generation of hybrid materials with improved properties.

     

Efficient solutions to robust, semi-implicit discretizations of the immersed boundary method

The immersed boundary method is a versatile tool for the investigation of flow-structure interaction. In a large number of applications, the immersed boundaries or structures are very stiff and strong tangential forces on these interfaces induce a well-known, severe time-step restriction for explicit discretizations. This excessive stability constraint can be removed with fully implicit or suitable semi-implicit schemes but at a seemingly prohibitive computational cost. While economical alternatives have been proposed recently for some special cases, there is a practical need for a computationally efficient approach that can be applied more broadly. In this context, we revisit a robust semi-implicit discretization introduced by Peskin in the late 1970s which has received renewed attention recently. This discretization, in which the spreading and interpolation operators are lagged, leads to a linear system of equations for the interface configuration at the future time, when the interfacial force is linear. However, this linear system is large and dense and thus it is challenging to streamline its solution. Moreover, while the same linear system or one of similar structure could potentially be used in Newton-type iterations, nonlinear and highly stiff immersed structures pose additional challenges to iterative methods. In this work, we address these problems and propose cost-effective computational strategies for solving Peskin’s lagged-operators type of discretization. We do this by first constructing a sufficiently accurate approximation to the system’s matrix and we obtain a rigorous estimate for this approximation. This matrix is expeditiously computed by using a combination of pre-calculated values and interpolation. The availability of a matrix allows for more efficient matrix–vector products and facilitates the design of effective iterative schemes. We propose efficient iterative approaches to deal with both linear and nonlinear interfacial forces and simple or complex immersed structures with tethered or untethered points. One of these iterative approaches employs a splitting in which we first solve a linear problem for the interfacial force and then we use a nonlinear iteration to find the interface configuration corresponding to this force. We demonstrate that the proposed approach is several orders of magnitude more efficient than the standard explicit method. In addition to considering the standard elliptical drop test case, we show both the robustness and efficacy of the proposed methodology with a 2D model of a heart valve.     

Three-dimensional,fully adaptive simulations of phase-field fluid models

We present an efficient numerical methodology for the 3D computation of incompressible multi-phase flows described by conservative phase-field models. We focus here on the case of density matched fluids with different viscosity (Model H). The numerical method employs adaptive mesh refinements (AMR) in concert with an efficient semi-implicit time discretization strategy and a linear, multi-level multigrid to relax high order stability constraints and to capture the flow’s disparate scales at optimal cost. Only five linear solvers are needed per time-step. Moreover, all the adaptive methodology is constructed from scratch to allow a systematic investigation of the key aspects of AMR in a conservative, phase-field setting. We validate the method and demonstrate its capabilities and efficacy with important examples of drop deformation, Kelvin–Helmholtz instability, and flow-induced drop coalescence.     

Fourier–Padé Approximants for Nikishin Systems

We study type I Fourier–Padé approximation for certain systems of functions formed by the Cauchy transform of finite Borel measures supported on bounded intervals of the real line. This construction is similar to type I Hermite–Padé approximation. Instead of power series expansions of the functions in the system, we take their development in a series of orthogonal polynomials. We give the exact rate of convergence of the corresponding approximants. The answer is expressed in terms of the extremal solution of an associated vector-valued equilibrium problem for the logarithmic potential.      

Coupled flow-polymer dynamics via statistical field theory: Modeling and computation

Field-theoretic models, which replace interactions between polymers with interactions between polymers and one or more conjugate fields, offer a systematic framework for coarse-graining of complex fluids systems. While this approach has been used successfully to investigate a wide range of polymer formulations at equilibrium, field-theoretic models often fail to accurately capture the non-equilibrium behavior of polymers, especially in the early stages of phase separation. Here the “two-fluid” approach serves as a useful alternative, treating the motions of fluid components separately in order to incorporate asymmetries between polymer molecules. In this work we focus on the connection of these two theories, drawing upon the strengths of each of the approaches in order to couple polymer microstructure with the dynamics of the flow in a systematic way. For illustrative purposes we work with an inhomogeneous melt of elastic dumbbell polymers, though our methodology will apply more generally to a wide variety of inhomogeneous systems. First we derive the model, incorporating thermodynamic forces into a two-fluid model for the flow through the introduction of conjugate chemical potential and elastic strain fields for the polymer density and stress. The resulting equations are composed of a system of fourth order PDEs coupled with a non-linear, non-local optimization problem to determine the conjugate fields. The coupled system is severely stiff and with a high degree of computational complexity. Next, we overcome the formidable numerical challenges posed by the model by designing a robust semi-implicit method based on linear asymptotic behavior of the leading order terms at small scales, by exploiting the exponential structure of global (integral) operators, and by parallelizing the non-linear optimization problem. The semi-implicit method effectively removes the fourth order stability constraint associated with explicit methods and we observe only a first order time-step restriction. The algorithm for solving the non-linear optimization problem, which takes advantage of the form of the operators being optimized, reduces the overall simulation time by several orders of magnitude. We illustrate the methodology with several examples of phase separation in an initially quiescent flow.     

A fast,robust, and non-stiff Immersed Boundary Method

We propose a fast and non-stiff approach for the solutions of the Immersed Boundary Method, for Newtonian, incompressible flows in two or three dimensions. The proposed methodology is built on a robust semi-implicit discretization introduced by Peskin in the late 70s which is solved efficiently through the novel use of a fast, treecode strategy to compute flow-structure interactions. Optimal multipole-type expansions are performed numerically by solving a least squares problem with a new, fast iterative algorithm. The new Immersed Boundary Method is particularly well suited for three-dimensional applications and/or for problems where the number of immersed boundary points is large. We demonstrate the efficacy and superiority of the method over existing approaches with two simple but illustrative examples in 3D.     

Computation of multiphase systems with phase field models

Phase field models offer a systematic physical approach for investigating complex multiphase systems behaviors such as near-critical interfacial phenomena, phase separation under shear, and microstructure evolution during solidification. However, because interfaces are replaced by thin transition regions (diffuse interfaces), phase field simulations require resolution of very thin layers to capture the physics of the problems studied. This demands robust numerical methods that can efficiently achieve high resolution and accuracy, especially in three dimensions. We present here an accurate and efficient numerical method to solve the coupled Cahn–Hilliard/Navier–Stokes system, known as Model H, that constitutes a phase field model for density-matched binary fluids with variable mobility and viscosity. The numerical method is a time-split scheme that combines a novel semi-implicit discretization for the convective Cahn–Hilliard equation with an innovative application of high-resolution schemes employed for direct numerical simulations of turbulence. This new semi-implicit discretization is simple but effective since it removes the stability constraint due to the nonlinearity of the Cahn–Hilliard equation at the same cost as that of an explicit scheme. It is derived from a discretization used for diffusive problems that we further enhance to efficiently solve flow problems with variable mobility and viscosity. Moreover, we solve the Navier–Stokes equations with a robust time-discretization of the projection method that guarantees better stability properties than those for Crank–Nicolson-based projection methods. For channel geometries, the method uses a spectral discretization in the streamwise and spanwise directions and a combination of spectral and high order compact finite difference discretizations in the wall normal direction. The capabilities of the method are demonstrated with several examples including phase separation with, and without, shear in two and three dimensions. The method effectively resolves interfacial layers of as few as three mesh points. The numerical examples show agreement with analytical solutions and scaling laws, where available, and the 3D simulations, in the presence of shear, reveal rich and complex structures, including strings.