Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation

Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.     

Convergence acceleration by self‐adjusted time stepsize using Bi‐CGSTAB method for turbulent separated flow computation

Poor convergence behavior is usually encountered when numerical computations on turbulent separated flow are performed. A design of self‐adjusted stepsize concept both in time span and spatial coordinate systems to achieve faster convergence is demonstrated in this study. The determination of the time stepsize based on the concept of minimization of residuals using the Bi‐CGSTAB algorithm is proposed. The numerical results show that the time stepsize adjusted by the proposed method indeed improves the convergence rate for turbulent separated flow computations using advanced turbulence models in low‐Reynolds number forms. Copyright © 2002 John Wiley & Sons, Ltd.     

Comparisons of TVD schemes for turbulent transonic projectile aerodynamics computations with a two-equation model of turbulence

The development of a computer program to solve the axisymmetric full Navier--Stokes equations with k-ε two-equation model of turbulence using various total variation diminishing (TVD) schemes is the primary interest of this study. The computations are performed for the turbulent, transonic, viscous flow over a projectile with/without supporting sting at zero angle of attack. The predicted results, as well as the convergence characteristics, by various TVD schemes are compared with each other. The results show that the TVD schemes of higher-order accuracy do have influence on the regions of high gradients such as shock, base corner and base flow. However, the schemes of third-order accuracy do not necessarily improve the agreement with measured data (which is not available on the base) than that of second-order accuracy, but surely generate apparent different result of base flow. The supporting sting on the projectile base will complicate the base flow and the existence of the sting will slightly shift the shock location and slightly change the flow field after the shock. More iteration steps are needed to get the converged results in the computation for the projectile with sting.     

Convergence acceleration by varying time‐step size using Bi‐CGSTAB method for turbulent flow computation

A design of varying step size approach both in time span and spatial coordinate systems to achieve fast convergence is demonstrated in this study. This method is based on the concept of minimization of residuals by the Bi‐CGSTAB algorithm, so that the convergence can be enforced by varying the time‐step size. The numerical results show that the time‐step size determined by the proposed method improves the convergence rate for turbulent computations using advanced turbulence models in low Reynolds‐number form, and the degree of improvement increases with the degree of the complexity of the turbulence models. © 2001 John Wiley & Sons, Inc. Numer Methods Partial Differential Eq 17: 454–474, 2001.     

EULERIAN–LAGRANGIAN COMPUTATIONS ON PHASE DISTRIBUTION OF TWO-PHASE BUBBLY FLOWS

A comprehensively theoretical model is developed and numerically solved to investigate the phase distribution phenomena in a two-dimensional, axisymmetric, developing, two-phase bubbly flow. The Eulerian approach treats the fluid phase as a continuum and solved Eulerian conservation equations for the liquid phase. The Lagrangian bubbles are tracked by solving the equation of motion for the gas phase. The interphase momentum changes are included in the equations. The numerical model successfully predicts detailed flow velocity profiles for both liquid and gas phases. The development of the wall-peaking phenomenon of the void fraction and velocity profiles is also characterized for the developing flow. For 42 experiments in which the mean void fraction is less than 20 per cent, numerical calculations demonstrate that the predictions agree well with Liu's experimental data. © 1997 by John Wiley & Sons, Ltd.     

Microsized 2D protein arrays immobilized by micro-stamps and micro-wells for disease diagnosis and drug screening

A novel method of protein array immobilization, using micro stamps to pick up proteins from micro wells and deposit them on to a bio-absorption chip, has been developed. This method can potentially transfer several protein spots on to an organized array for applications such as disease diagnosis and drug screening by parallel biological or chemical processes. Fabrication of the micro stamp and the micro well arrays involves thick-photoresist lithography, bulk micromachining, and a molding process, whereas fabrication of the bio-absorption chip involves amino-modification by use of APTS (aminopropyItrimethoxysilane) and surface activation by use of BS3 (bis-sulfosuccinimidyl suberate). Successful transfer of protein on to the bio-absorption surface using the micro stamp-well array has been demonstrated. The size variation between different stamping spots has been shown to be less than 10%, and the APTS-BS3 surface has also been proved to bind the protein efficiently. Appreciable protein retention was achieved during 6-h washing, which shows the binding strength of the bio-absorption surface is sufficient for protein processing.     

Complexation of cationic polyelectrolyte with anionic phospholipid vesicles: Concentration, molecular weight and salt effects

The influence of cationic poly(diallyldimethylammonium chloride) on the morphology and phase behavior of anionic phospholipid vesicles was investigated using differential scanning calorimetry, fluorescent microscopy and light scattering technique. A wide range of polymer concentration has been examined for the first time. The polycation can bind electrostatically to the vesicles to compensate, neutralize and reverse the vesicular charge, depending on the molar ratio of cationic to anionic group R. For R<1, charge compensation weakened the electrostatic repulsion between the lipid molecules, leading to formation of polymer-modified vesicles, each with an increased number of bilayers. The bilayer exhibits a rising main phase transition temperature from a gel to liquid crystalline state. This behavior persisted until R≈1 around the neutralization condition, where the complexes became largest and precipitate. With R>1, charge reversal took place, the complex size reduced. Interestingly, the main phase transition temperature was found for the first time to shift back towards the original value in the absence of polymer for large enough R. Although the thermal behavior was nearly independent of the polymer molecular weight, the complex morphology could be different.     

Comparison of variants of the bi-conjugate gradient method for compressible Navier-Stokes solver with second-moment closure

Variants of the bi-conjugate gradient (Bi-CG) method are used to resolve the problem of slow convergence in CFD when it is applied to complex flow field simulation using higher-order turbulence models. In this study the Navier-Stokes and Reynolds stress transport equations are discretized with an implicit, total variation diminishing (TVD), finite volume formulation. The preconditioning technique of incomplete lower-upper (ILU) factorization is incorporated into the conjugate gradient square (CGS), bi-conjugate gradient stable (Bi-CGSTAB) and transpose-free quasi-minimal residual (TFQMR) algorithms to accelerate convergence of the overall itertive methods. Computations have been carried out for separated flow fields over transonic bumps, supersonic bases and supersonic compression corners. By comparisons of the convergence rate with each other and with the conventional approximate factorization (AF) method it is shown that the Bi-CGSTAB method gives the most efficient convergence rate among these methods and can speed up the CPU time by a factor of 2·4–6·5 as compared with the AF method. Moreover, the AF method may yield somewhat different results from variants of the Bi-CG method owing to the factorization error which introduces a higher level of convergence criterion.