We present a solver for the Poisson-Boltzmann equation and demonstrate its applicability for biomolecular electrostatics computation. The solver uses a level set framework to represent sharp, complex interfaces in a simple and robust manner. It also uses non-graded, adaptive octree grids which, in comparison to uniform grids, drastically decrease memory usage and runtime without sacrificing accuracy. The basic solver was introduced in earlier works [16,27], and here is extended to address biomolecular systems. First, a novel approach of calculating the solvent excluded and the solvent accessible surfaces is explained; this allows to accurately represent the location of the molecule’s surface. Next, a hybrid finite difference/finite volume approach is presented for discretizing the nonlinear Poisson-Boltzmann equation and enforcing the jump boundary conditions at the interface. Since the interface is implicitly represented by a level set function, imposing the jump boundary conditions is straightforward and efficient.

We report about a numerical algorithm based on the lattice Boltzmann method and its applications for simulations of turbulent convection in multi-phase flows. We discuss the issue of ’latent heat’ definition using a thermodynamically consistent pseudo-potential on the lattice. We present results of numerical simulations in 3D with and without boiling, showing the distribution of pressure, density and temperature fluctuations inside a convective cell.

We study compact finite difference methods for the Schrodinger-Poisson equation in a bounded domain and establish their optimal error estimates under proper regularity assumptions on wave function and external potential V(x). The Crank-Nicolson compact finite difference method and the semi-implicit compact finite difference method are both of order Ҩ(h4 + τ2) in discrete l2,H1 and l∞ norms with mesh size h and time step t. For the errors ofcompact finite difference approximation to the second derivative andPoisson potential are nonlocal, thus besides the standard energy method and mathematical induction method, the key technique in analysisis to estimate the nonlocal approximation errors in discrete l∞ and H1 norm by discrete maximum principle of elliptic equation and properties of some related matrix. Also some useful inequalities are established in this paper. Finally, extensive numerical re-sults are reported to support our error estimates of the numerical methods.

High-order interpolation algorithms for charge conservation in Particle-in-Cell (PIC) simulations are presented. The methods are valid for the case that a particle trajectory is a zigzag line. The second-order and third-order algorithms which can be applied to any even-order and odd-order are discussed in this paper, respectively. Several test simulations are performed to demonstrate their validity in two-dimensional PIC code. Compared with the simulation results of one-order, high-order algorithms have advantages in computation precision and enlarging the grid scales which reduces the CPU time.

Numerical solutions of a non-Fickian diffusion equation belonging to a hyperbolic type are presented in one space dimension. The Brownian particle modelled by this diffusion equation is subjected to a symmetric periodic potential whose spatial shape can be varied by a single parameter. We consider a numerical method which consists of applying Laplace transform in time; we then obtain an elliptic diffusion equation which is discretized using a finite difference method. We analyze some aspects of the convergence of the method. Numerical results for particle density, flux and mean-square-displacement (covering both inertial and diffusive regimes) are presented.

A comparative study is conducted to evaluate three types of lattice Boltzmann equation (LBE) models for fluid flows with finite-sized particles, including the lattice Bhatnagar-Gross-Krook (BGK) model, the model proposed by Ladd [Ladd AJC, J. Fluid Mech., 271, 285-310 (1994); Ladd AJC, J. Fluid Mech., 271, 311-339 (1994)], and the multiple-relaxation-time (MRT) model. The sedimentation of a circular particle in a two-dimensional infinite channel under gravity is used as the first test problem. The numerical results of the three LBE schemes are compared with the theoretical results and existing data. It is found that all of the three LBE schemes yield reasonable results in general, although the BGK scheme and Ladd’s scheme give some deviations in some cases. Our results also show that the MRT scheme can achieve a better numerical stability than the other two schemes. Regarding the computational efficiency, it is found that the BGK scheme is the most superior one, while the other two schemes are nearly identical. We also observe that the MRT scheme can unequivocally reduce the viscosity dependence of the wall correction factor in the simulations, which reveals the superior robustness of the MRT scheme. The superiority of the MRT scheme over the other two schemes is also confirmed by the simulation of the sedimentation of an elliptical particle.

A search was made for possible half-metallic (HM) antiferromagnet (AFM) in all the double perovskites structures of Sr2BB'O6 where BB' pairs are any combination of 3d, 4d or 5d transition elements with the exception of La. Sr can also be replaced by Ca or Ba whenever HM-AFM was found and similar calculations were then performed in order to probe further possibilities. It was found that A2MoOsO6, A2TcReO6, A2CrRuO6, where A=Ca, Sr, Ba, are all potential candidates for HM-AFM. The AFM of A2BB'O6 comes from both the superexchange mechanism and the generalized double exchange mechanism via the B(t2g)-O2pπ-B'(t2g) coupling, With the latter also being the origin of their HM. Also considered were the effects of spin-orbit coupling (SOC) and correlation (+U) by introducing +SOC and +U corrections. It is found that the SOC effect has much less influence than the correlation effect on the HM property of the compounds. For A2TcReO6 and A2CrRuO6, after +U, they become nearly Mott-Insulators. In the future, it is hoped that there will be further experimental confirmation for these possible HM-AFM candidates.

A nonlocal continuum electrostatic model, defined as integro-differential equations, can significantly improve the classic Poisson dielectric model, but is too costly to be applied to large protein simulations. To sharply reduce the model’s complexity, a modified nonlocal continuum electrostatic model is presented in this paper for a protein immersed in water solvent, and then transformed equivalently as a system of partial differential equations. By using this new differential equation system, analytical solutions are derived for three different nonlocal ionic Born models, where a monoatomic ion is treated as a dielectric continuum ball with point charge either in the center or uniformly distributed on the surface of the ball. These solutions are analytically verified to satisfy the original integro-differential equations, thereby, validating the new differential equation system.

We present an efficient method to solve the time dependent Schrodinger equation for modeling the dynamics of diatomic molecules irradiated by intense ultrashort laser pulse without Born-Oppenheimer approximation. By introducing a variable prolate spheroidal coordinates and discrete variable representations of the Hamiltonian, we can accurately and efficiently simulate the motion of both electronic and molecular dynamics. The accuracy and convergence of this method are tested by simulating the molecular structure, photon ionization and high harmonic generation of H+2

Lattice Boltzmann simulations based on the Cahn-Hilliard diffuse interface approach are performed for droplet dynamics in viscous fluid under shear flow, where the degree of confinement between two parallel walls can play an important role. The effects of viscosity ratio, capillary number, Reynolds number, and confinement ratio on droplet deformation and break-up in moderately and highly confined shear flows are investigated.

Stochastic walk-on-spheres (WOS) algorithms for solving the linearized Poisson-Boltzmann equation (LPBE) provide several attractive features not available in traditional deterministic solvers: Gaussian error bars can be computed easily, the algorithm is readily parallelized and requires minimal memory and multiple solvent environments can be accounted for by reweighting trajectories. However, previously-reported computational times of these Monte Carlo methods were not competitive with existing deterministic numerical methods. The present paper demonstrates a series of numerical optimizations that collectively make the computational time of these Monte Carlo LPBE solvers competitive with deterministic methods. The optimization techniques used are to ensure that each atom’s contribution to the variance of the electrostatic solvation free energy is the same, to optimize the bias-generating parameters in the algorithm and to use an epsilon-approximate rather than exact nearest-neighbor search when determining the size of the next step in the Brownian motion when outside the molecule.

We study the static and dynamical behavior of the contact line between two fluids and a solid plate by means of the Lattice Boltzmann method (LBM). The different fluid phases and their contact with the plate are simulated by means of standard Shan-Chen models. We investigate different regimes and compare the multicomponent vs. the multiphase LBM models near the contact line. A static interface profile is attained with the multiphase model just by balancing the hydrostatic pressure (due to gravity) with a pressure jump at the bottom. In order to study the same problem with the multicomponent case we propose and validate an idea of a body force acting only on one of the two fluid components. In order to reproduce results matching an infinite bath, boundary conditions at the bath side play a key role. We quantitatively compare open and wall boundary conditions and study their influence on the shape of the meniscus against static and lubrication theory solution.

We have introduced a fully second order IMplicit/EXplicit (IMEX) time in-tegration technique for solving the compressible Euler equations plus nonlinear heat conduction problems (also known as the radiation hydrodynamics problems) in Kadioglu et al., J. Comp. Physics [22,24]. In this paper, we study the implications when this method is applied to the incompressible Navier-Stokes (N-S) equations. The IMEX method is applied to the incompressible flow equations in the following manner. The hyperbolic terms of the flow equations are solved explicitly exploiting the well understood explicit schemes. On the other hand, an implicit strategy is employed for the non-hyperbolic terms. The explicit part is embedded in the implicit step in such a way that it is solved as part of the non-linear function evaluation within the framework of the Jacobian-Free Newton Krylov (JFNK) method [8,29,31]. This is done to obtain a self-consistent implementation of the IMEX method that eliminates the potential order reduction in time accuracy due to the specific operator separation. We employ a simple yet quite effective fractional step projection methodology (similar to those in [11,19,21,30]) as our preconditioner inside the JFNK solver. We present results from several test calculations. For each test, we show second order time convergence. Finally, we present a study for the algorithm performance of the JFNK solver with the new projection method based preconditioner.

The polynomial chaos expansion (PCE) is an efficient numerical method for performing a reliability analysis. It relates the output of a nonlinear system with the uncertainty in its input parameters using a multidimensional polynomial approximation (the so-called PCE). Numerically, such an approximation can be obtained by using a regression method with a suitable design of experiments. The cost of this approximation depends on the size of the design of experiments. If the design of experiments is large and the system is modeled with a computationally expensive FEA (Finite Element Analysis) model, the PCE approximation becomes unfeasible. The aim of this work is to propose an algorithm that generates efficiently a design of experiments of a size defined by the user, in order to make the PCE approximation computationally feasible. It is an optimization algorithm that seeks to find the best design of experiments in the D-optimal sense for the PCE. This algorithm is a coupling between genetic algorithms and the Fedorov exchange algorithm. The efficiency of our approach in terms of accuracy and computational time reduction is compared with other existing methods in the case of analytical functions and finite element based functions.

Numerical simulation of two-phase flow in fractured karst reservoirs is still a challenging issue. The triple-porosity model is the major approach up to now. However, the triple-continuum assumption in this model is unacceptable for many cases. In the present work, an efficient numerical model has been developed for immiscible two-phase flow in fractured karst reservoirs based on the idea of equivalent continuum representation. First, based on the discrete fracture-vug model and homogenization theory, the effective absolute permeability tensors for each grid blocks are calculated. And then an analytical procedure to obtain a pseudo relative permeability curves for a grid block containing fractures and cavities has been successfully implemented. Next, a full-tensor simulator has been designed based on a hybrid numerical method (combining mixed finite element method and finite volume method). A simple fracture system has been used to demonstrate the validity of our method. At last, we have used the fracture and cavity statistics data from TAHE outcrops in west China, effective permeability values and other parameters from our code, and an equivalent continuum simulator to calculate the water flooding profiles for more realistic systems.

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt-bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism.

The gas-kinetic scheme is applied to a depth-integrated continuum model for avalanche flows, namely the Savage-Hutter model. In this method, the continuum fluxes are calculated based on the pseudo particle motions which are relaxed from nonequilibrium to equilibrium states. The processes are described by the Bhatnagar-Gross-Krook (BGK) equation. The benefit of this scheme is its capability to resolve shock discontinuities sharply and to handle the vacuum state without special treatments. Because the Savage-Hutter equation bears an anisotropic stress on the tangential space of the topography, the equilibrium distribution function of the microscopic particles are shown to be bi-Maxwellian. These anisotropic stresses are the key to preserve the coordinate objectivity in the Savage-Hutter model. The effect of the anisotropic stress is illustrated by two examples: an axisymmetric dam break and a finite mass sliding on an inclined plane chute. It is found that the propagation of the flow fronts significantly depends on the orientation of the principal axes of the tangential stresses.

A lattice Boltzmann model for the study of advection-diffusion-reaction (ADR) problems is proposed. Via multiscale expansion analysis, we derive from the LB model the resulting macroscopic equations. It is shown that a linear equilibrium distribution is sufficient to produce ADR equations within error terms of the order of the Mach number squared. Furthermore, we study spatially varying structures arising from the interaction of advective transport with a cubic autocatalytic reaction-diffusion process under an imposed uniform flow. While advecting all the present species leads to trivial translation of the Turing patterns, differential advection leads to flow induced instability characterized with traveling stripes with a velocity dependent wave vector parallel to the flow direction. Predictions from a linear stability analysis of the model equations are found to be in line with these observations.

In this paper, hp-adaptive finite element methods are studied for time-harmonic Maxwell’s equations. We propose the parallel hp-adaptive algorithms on conforming unstructured tetrahedral meshes based on residual-based a posteriori error estimates. Extensive numerical experiments are reported to investigate the efficiency of the hp-adaptive methods for point singularities, edge singularities, and an engineering benchmark problem of Maxwell’s equations. The hp-adaptive methods show much better performance than the h-adaptive method.

The variable high-order multiblock overlapping (overset) grids method of Sjögreen & Yee [CiCP, Vol. 5, 2009] for a perfect gas has been extended to nonequilibrium flows. This work makes use of the recently developed high-order well-balanced shock-capturing schemes and their filter counterparts [Wang et al., J. Comput. Phys., 2009, 2010] that exactly preserve certain non-trivial steady state solutions of the chemical nonequilibrium governing equations. Multiscale turbulence with strong shocks and flows containing both steady and unsteady components is best treated by mixing of numerical methods and switching on the appropriate scheme in the appropriate subdomains of the flow fields, even under the multiblock grid or adaptive grid refinement framework. While low dissipative sixth- or higher-order shock-capturing filter methods are appropriate for unsteady turbulence with shocklets, second- and third- order shock-capturing methods are more effective for strong steady or nearly steady shocks in terms of convergence. It is anticipated that our variable high-order overset grid framework capability with its highly modular design will allow for an optimum synthesis of these new algorithms in such a way that the most appropriate spatial discretizations can be tailored for each particular region of the flow. In this paper some of the latest developments in single block high-order filter schemes for chemical nonequilibrium flows are applied to overset grid geometries. The numerical approach is validated on a number of test cases characterized by hypersonic conditions with strong shocks, including the reentry flow surrounding a 3D Apollo-like NASA Crew Exploration Vehicle that might contain mixed steady and unsteady components, depending on the flow conditions.