A finite difference method which is second-order accurate in time and in space is proposed for two-dimensional fractional percolation equations. Using the Fourier transform, a general approximation for the mixed fractional derivatives is analyzed. An approach based on the classical Crank-Nicolson scheme combined with the Richardson extrapolation is used to obtain temporally and spatially second-order accurate numerical estimates. Consistency, stability and convergence of the method are established. Numerical experiments illustrating the effectiveness of the theoretical analysis are provided.

Plasma waves with frequencies close to the particular gyrofrequencies of the charged particles in the plasma lose energy due to cyclotron damping. We briefly discuss the gyro-resonance of low frequency plasma waves and ions particularly with regard to particle-in-cell (PiC) simulations. A setup is outlined which uses artificially excited waves in the damped regime of the wave mode's dispersion relation to track the damping of the wave's electromagnetic fields. Extracting the damping rate directly fromthe field data in real or Fourier space is an intricate and non-trivial task. We therefore present a simple method of obtaining the damping rate Γ from the simulation data. This method is described in detail, focusing on a step-by-step explanation of the course of actions. In a first application to a test simulation we find that the damping rates obtained from this simulation generally are in good agreement with theoretical predictions. We then compare the results of one-, two- and three-dimensional simulation setups and simulations with different physical parameter sets.

This paper concerns the analytic structure of the self-consistent field theory (SCFT) energy functional of multicomponent block copolymer systems which contain more than two chemically distinct blocks. The SCFT has enjoyed considered success and wide usage in investigation of the complex phase behavior of block copolymers. It is well-known that the physical solutions of the SCFT equations are saddle points, however, the analytic structure of the SCFT energy functional has received little attention over the years. A recent work by Fredrickson and collaborators [see the monograph by Fredrickson, The Equilibrium Theory of Inhomogeneous Polymers, (2006), pp. 203–209] has analysed the mathematical structure of the field energy functional for polymeric systems, and clarified the index-1 saddle point nature of the problem caused by the incompressible constraint. In this paper, our goals are to draw further attention to multicomponent block copolymers utilizing the Hubbard-Stratonovich transformation used by Fredrickson and co-workers. We firstly show that the saddle point character of the SCFT energy functional of multicomponent block copolymer systems may be high index, not only produced by the incompressible constraint, but also by the Flory-Huggins interaction parameters. Our analysis will be beneficial to many theoretical studies, such as the nucleation theory of ordered phases, the mesoscopic dynamics. As an application, we utilize the discovery to develop the gradient-based iterative schemes to solve the SCFT equations, and illustrate its performance through several numerical experiments taking ABC star triblock copolymers as an example.

This paper presents a numerical and experimental study on hydrodynamic behavior of thin liquid films in rectangular domains. Three-dimensional computer simulations were performed using the lattice Boltzmann equation method (LBM). The liquid films laying on solid and liquid substrates are considered. The rupture of liquid films in computations is initiated via the thermocapillary (Marangoni) effect by applying an initial spatially localized temperature perturbation. The rupture scenario is found to depend on the shape of the temperature distribution and on the wettability of the solid substrate. For a wettable solid substrate, complete rupture does not occur: a residual thin liquid film remains at the substrate in the region of pseudo-rupture. For a non-wettable solid substrate, a sharp-peaked axisymmetric temperature distribution induces the rupture at the center of symmetry where the temperature is maximal. Axisymmetric temperature distribution with a flat-peaked temperature profile initiates rupture of the liquid film along a circle at some distance from the center of symmetry. The outer boundary of the rupture expands, while the inner liquid disk transforms into a toroidal figure and ultimately into an oscillating droplet.

We also apply the LBM to simulations of an evolution of one or two holes in liquid films for two-layer systems of immiscible fluids in a rectangular cell. The computed patterns are successfully compared against the results of experimental visualizations. Both the experiments and the simulations demonstrate that the initially circular holes evolved in the rectangular cell undergoing drastic changes of their shape under the effects of the surface tension and gravity. In the case of two interacting holes, the disruption of the liquid bridge separating two holes is experimentally observed and numerically simulated.

We present a systematic derivation of a model based on the central moment lattice Boltzmann equation that rigorously maintains Galilean invariance of forces to simulate inertial frame independent flow fields. In this regard, the central moments, i.e. moments shifted by the local fluid velocity, of the discrete source terms of the lattice Boltzmann equation are obtained by matching those of the continuous full Boltzmann equation of various orders. This results in an exact hierarchical identity between the central moments of the source terms of a given order and the components of the central moments of the distribution functions and sources of lower orders. The corresponding source terms in velocity space are then obtained from an exact inverse transformation due to a suitable choice of orthogonal basis for moments. Furthermore, such a central moment based kinetic model is further extended by incorporating reduced compressibility effects to represent incompressible flow. Moreover, the description and simulation of fluid turbulence for full or any subset of scales or their averaged behavior should remain independent of any inertial frame of reference. Thus, based on the above formulation, a new approach in lattice Boltzmann framework to incorporate turbulence models for simulation of Galilean invariant statistical averaged or filtered turbulent fluid motion is discussed.

We present an accelerated method for stochastically simulating the dynamics of heterogeneous cell populations. The algorithm combines a Monte Carlo approach for simulating the biochemical kinetics in single cells with a constant-number Monte Carlo method for simulating the reproductive fitness and the statistical characteristics of growing cell populations. To benchmark accuracy and performance, we compare simulation results with those generated from a previously validated population dynamics algorithm. The comparison demonstrates that the accelerated method accurately simulates population dynamics with significant reductions in runtime under commonly invoked steady-state and symmetric cell division assumptions. Considering the increasing complexity of cell population models, the method is an important addition to the arsenal of existing algorithms for simulating cellular and population dynamics that enables efficient, coarse-grained exploration of parameter space.

A new approach for reducing error of the volume penalization method is proposed. The mask function is modified by shifting the interface between solid and fluid by toward the fluid region, where v and η are the viscosity and the permeability, respectively. The shift length is derived from the analytical solution of the one-dimensional diffusion equation with a penalization term. The effect of the error reduction is verified numerically for the one-dimensional diffusion equation, Burgers’ equation, and the two-dimensional Navier-Stokes equations. The results show that the numerical error is reduced except in the vicinity of the interface showing overall second-order accuracy, while it converges to a non-zero constant value as the number of grid points increases for the original mask function. However, the new approach is effectivewhen the grid resolution is sufficiently high so that the boundary layer,whose width is proportional to , is resolved. Hence, the approach should be used when an appropriate combination of ν and η is chosen with a given numerical grid.

The lattice Boltzmann method is applied to the investigations of the diffusivity and the permeability in the gas diffusion layer (GDL) of the polymer electrolyte fuel cell (PEFC). The effects of the configuration of water droplets, the porosity of the GDL, the viscosity ratio of water to air, and the surface wettability of the GDL are investigated. From the simulations under the PEFC operating conditions, it is found that the heterogeneous water network and the high porosity improve the diffusivity and the permeability, and the hydrophobic surface decreases the permeability.

This paper presents an exponential compact higher order scheme for Convection-Diffusion Equations (CDE) with variable and nonlinear convection coefficients. The scheme is for one-dimensional problems and produces a tri-diagonal system of equations which can be solved efficiently using Thomas algorithm. For two-dimensional problems, the scheme produces an accuracy over a compact nine point stencil which can be solved using any line iterative approach with alternate direction implicit procedure. The convergence of the iterative procedure is guaranteed as the coefficient matrix of the developed scheme satisfies the conditions required to be positive. Wave number analysis has been carried out to establish that the scheme is comparable in accuracy with spectral methods. The higher order accuracy and better rate of convergence of the developed scheme have been demonstrated by solving numerous model problems for one and two-dimensional CDE, where the solutions have the sharp gradient at the solution boundary.

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 structural and functional description of protein-protein complexes and their comprehension is a key concept, not only to increase the scientific knowledge in basic terms but also for the application to the biomedical and pharmaceutical industry. The binding association between proteins is nowadays attribute to a few key residues at the interface – the hot-spots. The complex between the RNase inhibitor (RI) and RNaseA protein provides an excellent system to study the role of the functional epitope as it is essential in various molecular recognition processes and constitute one of the tightest complexes known. An energetic pattern of the interface is accomplished by computational alanine scanning mutagenesis and a dynamical characterization is accomplished by a detailed study of the molecular dynamical simulations. A special emphasis is given to the role of solvation across the interface and the shielding of warm-and hot-spots from water.

A novel mesh deformation technique is developed based on the Delaunay graph mapping method and the inverse distance weighting (IDW) interpolation. The algorithm maintains the advantages of the efficiency of Delaunay graph mapping mesh deformation while it also possesses the ability of better controlling the near surface mesh quality. The Delaunay graph is used to divide the mesh domain into a number of sub-domains. On each sub-domain, the inverse distance weighting interpolation is applied, resulting in a similar efficiency as compared to the fast Delaunay graph mapping method. The paper will show how the near-wall mesh quality is controlled and improved by the new method

Discontinuous Galerkin (DG) and matrix-free finite element methods with a novel projective pressure estimation are combined to enable the numerical modeling of magma dynamics in 2D and 3D using the library deal.II. The physical model is an advection-reaction type system consisting of two hyperbolic equations to evolve porosity and soluble mineral abundance at local chemical equilibrium and one elliptic equation to recover global pressure. A combination of a discontinuous Galerkin method for the advection equations and a finite element method for the elliptic equation provide a robust and efficient solution to the channel regime problems of the physical system in 3D. A projective and adaptively applied pressure estimation is employed to significantly reduce the computational wall time without impacting the overall physical reliability in the modeling of important features of melt segregation, such as melt channel bifurcation in 2D and 3D time dependent simulations.

In this paper we develop a conservative local discontinuous Galerkin (LDG) method for the Schrödinger-Korteweg-de Vries (Sch-KdV) system, which arises in various physical contexts as a model for the interaction of long and short nonlinear waves. Conservative quantities in the discrete version of the number of plasmons, energy of the oscillations and the number of particles are proved for the LDG scheme of the Sch-KdV system. Semi-implicit time discretization is adopted to relax the time step constraint from the high order spatial derivatives. Numerical results for accuracy tests of stationary traveling soliton, and the collision of solitons are shown. Numerical experiments illustrate the accuracy and capability of the method.

In this paper, we develop an efficient numerical method based on the boundary integral equation formulation and new version of fast multipole method to solve the boundary value problem for the stress field associated with dislocations in a finite medium. Numerical examples are presented to examine the influence from material boundaries on dislocations.

By combining the characteristic method and the local discontinuous Galerkin method with carefully constructing numerical fluxes, variational formulations are established for time-dependent incompressible Navier-Stokes equations in ℝ2. The nonlinear stability is proved for the proposed symmetric variational formulation. Moreover, for general triangulations the priori estimates for the L2–norm of the errors in both velocity and pressure are derived. Some numerical experiments are performed to verify theoretical results.

This study aims to investigate turbulent plasma flow using the lattice Boltzmann (LB) method. A double population model D2Q9-D2Q4 is employed to calculate the plasma velocity and temperature fields. Along with the calculation process a conversion procedure is made between the LB and the physical unit systems, so that thermo-physical properties variation is fully accounted for and the convergence is checked in physical space. The configuration domain and the boundary condition treatment are selected based on the most cited studies in order to illustrate a realistic situation. The jet morphology analysis gives credible results by comparison with commonly published works. It was demonstrated also that accounting for the substrate as wall boundary condition modify greatly the flow and temperature structures with may affect absolutely the particles behavior during its in-flight in the hot gas.

In this work we consider a general notion of distributional sensitivity, which measures the variation in solutions of a given physical/mathematical system with respect to the variation of probability distribution of the inputs. This is distinctively different from the classical sensitivity analysis, which studies the changes of solutions with respect to the values of the inputs. The general idea is measurement of sensitivity of outputs with respect to probability distributions, which is a well-studied concept in related disciplines. We adapt these ideas to present a quantitative framework in the context of uncertainty quantification for measuring such a kind of sensitivity and a set of efficient algorithms to approximate the distributional sensitivity numerically. A remarkable feature of the algorithms is that they do not incur additional computational effort in addition to a one-time stochastic solver. Therefore, an accurate stochastic computation with respect to a prior input distribution is needed only once, and the ensuing distributional sensitivity computation for different input distributions is a post-processing step. We prove that an accurate numericalmodel leads to accurate calculations of this sensitivity, which applies not just to slowly-converging Monte-Carlo estimates, but also to exponentially convergent spectral approximations. We provide computational examples to demonstrate the ease of applicability and verify the convergence claims.

A globally hyperbolic moment system upto arbitrary order for the Wigner equation was derived in [6]. For numerically solving the high order hyperbolic moment system therein, we in this paper develop a preliminary numerical method for this system following the NRxx method recently proposed in [8], to validate the moment system of the Wigner equation. The method developed can keep both mass and momentum conserved, and the variation of the total energy under control though it is not strictly conservative. We systematically study the numerical convergence of the solution to the moment system both in the size of spatial mesh and in the order of the moment expansion, and the convergence of the numerical solution of the moment system to the numerical solution of the Wigner equation using the discrete velocity method. The numerical results indicate that the high order moment system in [6] is a valid model for the Wigner equation, and the proposed numerical method for the moment system is quite promising to carry out the simulation of the Wigner equation.

We show that an enslaved phase-separation front moving with diffusive speeds can leave alternating domains of increasing size in their wake. We find the size and spacing of these domains is identical to Liesegang patterns. For equal composition of the components we are able to predict the exact form of the pattern analytically. To our knowledge this is the first fully analytical derivation of the Liesegang laws. We also show that there is a critical value for C below which only two domains are formed. Our analytical predictions are verified by numerical simulations using a lattice Boltzmann method.