In 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].

We report an efficient phase field formalism to compute the stress distribution in polycrystalline materials with arbitrary elastic inhomogeneity and anisotropy. The dependence of elastic stiffness tensor on grain orientation is taken into account, and the elastic equilibrium equation is solved using a spectral iterative perturbation method. We discuss its applications to computing residual stress distribution in systems containing arbitrarily shaped cavities and cracks (with zero elastic modulus) and to determining the effective elastic properties of polycrystals and multilayered composites.

We 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.

The study of interactions between a high-power laser and atoms has been one of the fundamental and interesting topics in strong field physics for decades. Based on a nonperturbative model, ten years ago, we developed a set of programs to facilitate the study of interactions between a circularly polarized laser and atomic hydrogen. These programs included only contribution from the bound states of the hydrogen atom. However, as the laser intensity increases, contribution from continuum states to the excitation and ionization processes becomes larger and can no longer be neglected. Furthermore, because the original code is not able to add this contribution directly due to its many disadvantages, a major upgrade of the code is required before including the contribution from continuum states in future. In this paper, first we deduce some important formulas for contribution of continuum states and present modifications and tests for the upgraded code in detail. Second we show some comparisons among new results, old results from the original codes and the available experimental data. Overall the new result agrees with experimental data well. Last we present our calculation of above-threshold ionization (ATI) rate and compare it with a pertubative calculation. The comparison shows that our nonperturbative calculation can also produce ATI peak suppression.

Based on the study of two commonly used stochastic elliptic models: I:−∇· (a(x,ω)·∇u(x,ω))=f(x) and II:−∇·(a(x,ω)⋄∇u(x,ω))=f(x), we constructed a new stochastic elliptic model III: −∇· (a⁻¹)^⋄(−1)⋄∇u(x,ω))=f(x), in [20]. The difference between models I and II is twofold: a scaling factor induced by the way of applying the Wick product and the regularization induced by the Wick product itself. In [20], we showed that model III has the same scaling factor as model I. In this paper we present a detailed discussion about the difference between models I and III with respect to the two characteristic parameters of the random coefficient, i.e., the standard deviation $σ$ and the correlation length l_c. Numerical results are presented for both one- and two-dimensional cases

A detailed comparison of continuum and valence force field strain calculations in quantum-dot structures is presented with particular emphasis to boundary conditions, their implementation in the finite-element method, and associated implications for electronic states. The first part of this work provides the equation framework for the elastic continuum model including piezoelectric effects in crystal structures as well as detailing the Keating model equations used in the atomistic valence force field calculations. Given the variety of possible structure shapes, a choice of pyramidal, spherical and cubic-dot shapes is made having in mind their pronounced shape differences and practical relevance. In this part boundary conditions are also considered; in particular the relevance of imposing different types of boundary conditions is highlighted and discussed. In the final part, quantum dots with inhomogeneous indium concentration profiles are studied in order to highlight the importance of taking into account the exact In concentration profile for real quantum dots. The influence of strain, electric-field distributions, and material inhomogeneity of spherical quantum dots on electronic wavefunctions is briefly discussed.

We develop a continuum hydrodynamic model for two-phase immiscible flows that involve electroosmotic effect in an electrolyte and moving contact line at solid surfaces. The model is derived through a variational approach based on the Onsager principle of minimum energy dissipation. This approach was first presented in the derivation of a continuum hydrodynamic model for moving contact line in neutral two-phase immiscible flows (Qian, Wang, and Sheng, J. Fluid Mech. 564, 333–360 (2006)). Physically, the electroosmotic effect can be formulated by the Onsager principle as well in the linear response regime. Therefore, the same variational approach is applied here to the derivation of the continuum hydrodynamic model for charged two-phase immiscible flows where one fluid component is an electrolyte exhibiting electroosmotic effect on a charged surface. A phase field is employed to model the diffuse interface between two immiscible fluid components, one being the electrolyte and the other a nonconductive fluid, both allowed to slip at solid surfaces. Our model consists of the incompressible Navier-Stokes equation for momentum transport, the Nernst-Planck equation for ion transport, the Cahn-Hilliard phase-field equation for interface motion, and the Poisson equation for electric potential, along with all the necessary boundary conditions. In particular, all the dynamic boundary conditions at solid surfaces, including the generalized Navier boundary condition for slip, are derived together with the equations of motion in the bulk region. Numerical examples in two-dimensional space, which involve overlapped electric double layer fields, have been presented to demonstrate the validity and applicability of the model, and a few salient features of the two-phase immiscible electroosmotic flows at solid surface. The wall slip in the vicinity of moving contact line and the Smoluchowski slip in the electric double layer are both investigated.

In this paper, we study high order discretization methods for solving the Maxwell equations on hybrid triangle-quad meshes. We have developed high order finite edge element methods coupled with different high order time schemes and we compare results and efficiency for several schemes. We introduce in particular a class of simple high order low dissipation time schemes based on a modified Taylor expansion.

In this paper we study Bénard-Marangoni convection in confined containers where a thin fluid layer is heated from below. We consider containers with circular, square and hexagonal cross-sections. For Marangoni numbers close to the critical Marangoni number, the flow patterns are dominated by the appearance of the wellknown hexagonal convection cells. The main purpose of this computational study is to explore the possible patterns the system may end up in for a given set of parameters. In a series of numerical experiments, the coupled fluid-thermal system is started with a zero initial condition for the velocity and a random initial condition for the temperature. For a given set of parameters we demonstrate that the system can end up in more than one state. For example, the final state of the system may be dominated by a steady convection pattern with a fixed number of cells, however, the same system may occasionally end up in a steady pattern involving a slightly different number of cells, or it may end up in a state where most of the cells are stationary, while one or more cells end up in an oscillatory state. For larger aspect ratio containers, we are also able to reproduce dislocations in the convection pattern, which have also been observed experimentally. It has been conjectured that such imperfections (e.g., a localized star-like pattern) are due to small irregularities in the experimental setup (e.g., the geometry of the container). However, we show, through controlled numerical experiments, that such phenomena may appear under otherwise ideal conditions. By repeating the numerical experiments for the same non-dimensional numbers, using a different random initial condition for the temperature in each case, we are able to get an indication of how rare such events are. Next, we study the effect of symmetrizing the initial conditions. Finally, we study the effect of selected geometry deformations on the resulting convection patterns.

In this paper, an immersed interface method is presented to simulate the dynamics of inextensible interfaces in an incompressible flow. The tension is introduced as an augmented variable to satisfy the constraint of interface inextensibility, and the resulting augmented system is solved by the GMRES method. In this work, the arclength of the interface is locally and globally conserved as the enclosed region undergoes deformation. The forces at the interface are calculated from the configuration of the interface and the computed augmented variable, and then applied to the fluid through the related jump conditions. The governing equations are discretized on a MAC grid via a second-order finite difference scheme which incorporates jump contributions and solved by the conjugate gradient Uzawa-type method. The proposed method is applied to several examples including the deformation of a liquid capsule with inextensible interfaces in a shear flow. Numerical results reveal that both the area enclosed by interface and arclength of interface are conserved well simultaneously. These provide further evidence on the capability of the present method to simulate incompressible flows involving inextensible interfaces.

The coherent states approximation for one-dimensional multi-phased wave functions is considered in this paper. The wave functions are assumed to oscillate on a characteristic wave length O(ε) with ε≪1. A parameter recovery algorithm is first developed for single-phased wave function based on a moment asymptotic analysis. This algorithm is then extended to multi-phased wave functions. If cross points or caustics exist, the coherent states approximation algorithm based on the parameter recovery will fail in some local regions. In this case, we resort to the windowed Fourier transform technique, and propose a composite coherent states approximation method. Numerical experiments show that the number of coherent states derived by the proposed method is much less than that by the direct windowed Fourier transform technique. 

This paper further considers weighted essentially non-oscillatory (WENO) and Hermite weighted essentially non-oscillatory (HWENO) finite volume methods as limiters for Runge-Kutta discontinuous Galerkin (RKDG) methods to solve problems involving nonlinear hyperbolic conservation laws. The application discussed here is the solution of 3-D problems on unstructured meshes. Our numerical tests again demonstrate this is a robust and high order limiting procedure, which simultaneously achieves high order accuracy and sharp non-oscillatory shock transitions. 

A multi-hierarchy simulation model aiming magnetic reconnection studies is developed and improved in which macroscopic and microscopic physics are computed consistently and simultaneously. Macroscopic physics is solved by magnetohydrodynamics (MHD) algorithm, while microscopic dynamics is expressed by particle-in-cell (PIC) algorithm. The multi-hierarchy model relies on the domain decomposition method, and macro- and micro-hierarchies are interlocked smoothly by hand-shake scheme. As examination, plasma flow injection is simulated in the multi-hierarchy model. It is observed that plasmas flow from a macro-hierarchy to a micro-hierarchy across the magnetic field smoothly and continuously. 

Standard compact scheme and upwinding compact scheme have high order accuracy and high resolution, but cannot capture the shock which is a discontinuity. This work developed a modified upwinding compact scheme which uses an effective shock detector to block compact scheme to cross the shock and a control function to mix the flux with WENO scheme near the shock. The new scheme makes the original compact scheme able to capture the shock sharply and, more importantly, keep high order accuracy and high resolution in the smooth area which is particularly important for shock boundary layer and shock acoustic interactions. Numerical results show the scheme is successful for 2-D Euler and 2-D Navier-Stokes solvers. The examples include 2-D incident shock, 2-D incident shock and boundary layer interaction. The scheme is robust, which does not involve case related parameters.