A computational model of cell polarization and motility coupling mechanics and biochemistry

The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time scales, with reaction kinetics on the order of seconds, and the deformation and motion of the cell occurring on the order of minutes. The computational difficulty, even in 2D, resides in the fact that the problem is inherently one of deforming, non-stationary domains, bounded by an elastic perimeter, inside of which there is redistribution of biochemical signaling substances. Here we report the results of a computational scheme using the immersed boundary method to address this problem. We adopt a simple reaction-diffusion system that represents an internal regulatory mechanism controlling the polarization of a cell, and determining the strength of protrusion forces at the front of its elastic perimeter. Using this computational scheme we are able to study the effect of protrusive and elastic forces on cell shapes on their own, the distribution of the reaction-diffusion system in irregular domains on its own, and the coupled mechanical-chemical system. We find that this representation of cell crawling can recover important aspects of the spontaneous polarization and motion of certain types of crawling cells.     

固定化酶的反应扩散过程的靶波解

通过固定化酶的数学模型的数值模拟,发现其反应扩散过程是以靶波形式出现的。     

Finite difference reaction-diffusion systems with coupled boundary conditions and time delays

This paper is concerned with finite difference solutions of a coupled system of reaction-diffusion equations with nonlinear boundary conditions and time delays. The system is coupled through the reaction functions as well as the boundary conditions, and the time delays may appear in both the reaction functions and the boundary functions. The reaction-diffusion system is discretized by the finite difference method, and the investigation is devoted to the finite difference equations for both the time-dependent problem and its corresponding steady-state problem. This investigation includes the existence and uniqueness of a finite difference solution for nonquasimonotone functions, monotone convergence of the time-dependent solution to a maximal or a minimal steady-state solution for quasimonotone functions, and local and global attractors of the time-dependent system, including the convergence of the time-dependent solution to a unique steady-state solution. Also discussed are some computational algorithms for numerical solutions of the steady-state problem when the reaction function and the boundary function are quasimonotone. All the results for the coupled reaction-diffusion equations are directly applicable to systems of parabolic-ordinary equations and to reaction-diffusion systems without time delays.     

The method of upper and lower solutions for diffraction problems of quasilinear elliptic reaction-diffusion systems

The aim of this paper is to show the existence of solutions of the n-dimensional diffraction problem for weakly coupled quasilinear elliptic reaction-diffusion system. The coefficients of the equations under consideration are allowed to be discontinuous. We extend the method of upper and lower solutions for reaction-diffusion equations with continuous coefficients to the elliptic diffraction problem. An application of these results is given to the steady-state problem of Lotka-Volterra cooperation model with two cooperating species.     

Multiple solutions of a boundary-value problem in enzyme kinetics

In some immobilized enzyme systems the steady state of substrate concentration may suddenly change from a low profile to a high profile or vice versa when the physical parameters of the systems pass through certain critical values. This phenomenon is due to the transition from a unique solution to multiple solutions (or vice versa) of the enzyme reaction equation. This problem is studied by considering two physical parameters which represent the internal reaction mechanism and the external influence on the boundary of the reaction-diffusion medium. Both analytical and numerical results for the problem are presented. The analytical results include some sufficient conditions for the existence of multiple steady-state solutions as well as a unique solution. Various numerical results of the problem including time-dependent solutions and their convergence to steady-state solutions are given.     

A Finite Element Method for Singularly Perturbed Reaction—diffusion Problems

A finite element method is proposed for the sing ularly perturbed reaction-diffusion problem.An optimal error bound is derived,independent of the perturbation parameter.     

Shapes and measures

It is a well-known fact that a measurable set a shape can beconsidered as a measure; the aim of this work is to solve anoptimal-shape problem in such a way that it also answers thequestion of whether measures can be considered as shapes. Thispaper introduces a new method for solving problems of optimalshape design; by a process of embedding, the problem is replacedby another in which we seek to minimize a linear form over asubset of the product of two measure spaces defined by linearequalities. This minimization is global, and the theory allowsus to develop a computational method which enables us to findthe solution by finite-dimensional linear programming. The nearlyoptimal pair (C, dC) is obtained via the optimal pair of measuresby an approximation procedure. It is sometimes necessary toapply a standard minimization algorithm, because of some limitationsin the accuracy. Some examples are presented.     

Point condensations of a model for fungal development

We study the stationary solutions for a reaction-diffusion system of activator-inhibitor type which arises as a model for fungal development. Under the condition that the activator diffuses slowly and the inhibitor diffuses very quickly we rigorously construct solutions which show single peak pattern near the boundary or in the interior in the activator component and have nearly constant values in the other. We also establish the linear stability and instability of such solutions.     

Newton-Multigrid for Biological Reaction-Diffusion Problems with Random Coefficients

An algebraic Newton-multigrid method is proposed in order to efficiently solve systems of nonlinear reaction-diffusion problems with stochastic coefficients. These problems model the conversion of starch into sugars in growing apples. The stochastic system is first converted into a large coupled system of deterministic equations by applying a stochastic Galerkin finite element discretization. This method leads to high-order accurate stochastic solutions. A stable and high-order time discretization is obtained by applying a fully implicit Runge-Kutta method. After Newton linearization, a point-based algebraic multigrid solution method is applied. In order to decrease the computational cost, alternative multigrid preconditioners are presented. Numerical results demonstrate the convergence properties, robustness and efficiency of the proposed multigrid methods.     

An efficient solution method for rank two quasiconcave minimization problems

The technique of dimension reduction earlier developed by the first author is applied to the class of nonconvex minimization problems having the so called rank two property. This class includes in particular the problem of minimizing the product of two affine functions over a polytope. An efficient method for solving this class of problems is presented. Also some results of computational experiments with this method are discussed     

Linear multiplicative programming

An algorithm for solving a linear multiplicative programming problem (referred to as LMP) is proposed. LMP minimizes the product of two linear functions subject to general linear constraints. The product of two linear functions is a typical non-convex function, so that it can have multiple local minima. It is shown, however, that LMP can be solved efficiently by the combination of the parametric simplex method and any standard convex minimization procedure. The computational results indicate that the amount of computation is not much different from that of solving linear programs of the same size. In addition, the method proposed for LMP can be extended to a convex multiplicative programming problem (CMP), which minimizes the product of two convex functions under convex constraints.     

Numerical solution of two-dimensional reaction-diffusion Brusselator system

In this paper, polynomial based differential quadrature method (DQM) is applied for the numerical solution of a class of two-dimensional initial-boundary value problems governed by a non-linear system of partial differential equations. The system is known as the reaction-diffusion Brusselator system. The system arises in the modeling of certain chemical reaction-diffusion processes. In Brusselator system the reaction terms arise from the mathematical modeling of chemical systems such as in enzymatic reactions, and in plasma and laser physics in multiple coupling between modes. The numerical results reported for three specific problems. Convergence and stability of the method is also examined numerically.     

Models of unidirectional propagation in heterogeneous excitable media

Two differential equation models of excitable media (threshold and recovery kinetics) with solutions that exhibit unidirectional propagation are presented. It is shown that unidirectional propagation in heterogeneous excitable media with non-oscillatory kinetics can be initiated from homogeneous initial data. Simulations on a reaction-diffusion model with FitzHugh-Nagumo kinetics and spatially heterogeneous parameters yields a rotating wave on a one-dimensional circular spatial domain. An ordinary differential equation model with four semi-coupled excitable cells and heterogeneous parameters is analyzed to determine a critical parameter region over which unidirectional propagation may occur.     

Model simulation and experiments of flow and mass transport through a nano-material gas filter

A computational model for evaluating the performance of nano-material packed-bed filters was developed. The porous effects of the momentum and mass transport within the filter bed were simulated. For the momentum transport, an extended Ergun-type model was employed and the energy loss (pressure drop) along the packed-bed was simulated and compared with measurement. For the mass transport, a bulk adsorption model was developed to study the adsorption process (breakthrough behavior). Various types of porous materials and gas flows were tested in the filter system where the mathematical models used in the porous substrate were implemented and validated by comparing with experimental data and analytical solutions under similar conditions. Good agreements were obtained between experiments and model predictions.     

Mobile and immobile gaseous transport: Embedded analytical solutions to finite volume methods

The motivation is driven by deposition processes based on chemical vapor problems. The underlying model problem is based on coupled transport–reaction equations with mobile and immobile areas. We deal with systems of ordinary and partial differential equations. Such equation systems are delicate to solve and we introduce a novel solver method, that takes into account ways to solve analytically parts of the transport and reaction equations. The main idea is to embed the analytical and semianalytical solutions, which can then be explicitly given to standard numerical schemes of higher order. The numerical scheme is based on flux‐based characteristic methods, which is a finite volume method. Such a method is an attractive alternative to the standard numerical schemes, which fully discretize the full equations. We instead reduce the computational time while embedding fast computable analytical parts. Here, we can accelerate the solver process, with a priori explicitly given solutions. We will focus on the derivation of the analytical solutions for general and special solutions of the characteristic methods that are embedded into a finite volume method. In the numerical examples, we illustrate the higher‐order method for different benchmark problems. Finally, the method is verified with realistic results. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2012     

An adaptive insertion algorithm for the single-vehicle dial-a-ride problem with narrow time windows

The dial-a-ride problem (DARP) is a widely studied theoretical challenge related to dispatching vehicles in demand-responsive transport services, in which customers contact a vehicle operator requesting to be carried from specified origins to specified destinations. An important subproblem arising in dynamic dial-a-ride services can be identified as the single-vehicle DARP, in which the goal is to determine the optimal route for a single vehicle with respect to a generalized objective function. The main result of this work is an adaptive insertion algorithm capable of producing optimal solutions for a time constrained version of this problem, which was first studied by Psaraftis in the early 1980s. The complexity of the algorithm is analyzed and evaluated by means of computational experiments, implying that a significant advantage of the proposed method can be identified as the possibility of controlling computational work smoothly, making the algorithm applicable to any problem size.     

Measure theoretical approach for optimal shape design of a nozzle

In this paper we present a new method for designing a nozzle. In fact the problem is to find the optimal domain for the solution of a linear or nonlinear boundary value PDE, where the boundary condition is defined over an unspecified domain. By an embedding process, the problem is first transformed to a new shape-measure problem, and then this new problem is replaced by another in which we seek to minimize a linear form over a subset of linear equalities. This minimization is global, and the theory allows us to develop a computational method to find the solution by a finite-dimensional linear programming problem.     

Two-level decomposition algorithm for crew rostering problems with fair working condition

A typical railway crew scheduling problem consists of two phases: a crew pairing problem to determine a set of crew duties and a crew rostering problem. The crew rostering problem aims to find a set of rosters that forms workforce assignment of crew duties and rest periods satisfying several working regulations. In this paper, we present a two-level decomposition approach to solve railway crew rostering problem with the objective of fair working condition. To reduce computational efforts, the original problem is decomposed into the upper-level master problem and the lower-level subproblem. The subproblem can be further decomposed into several subproblems for each roster. These problems are iteratively solved by incorporating cuts into the master problem. We show that the relaxed problem of the master problem can be formulated as a uniform parallel machine scheduling problem to minimize makespan, which is NP-hard. An efficient branch-and-bound algorithm is applied to solve the master problem. Effective valid cuts are developed to reduce feasible search space to tighten the duality gap. Using data provided by the railway company, we demonstrate the effectiveness of the proposed method compared with that of constraint programming techniques for large-scale problems through computational experiments.     

Front motion in the parabolic reaction-diffusion problem

A singularly perturbed initial-boundary value problem is considered for a parabolic equation known in applications as the reaction-diffusion equation. An asymptotic expansion of solutions with a moving front is constructed, and an existence theorem for such solutions is proved. The asymptotic expansion is substantiated using the asymptotic method of differential inequalities, which is extended to the class of problems under study. The method is based on well-known comparison theorems and is a development of the idea of using formal asymptotics for the construction of upper and lower solutions in singularly perturbed problems with internal and boundary layers.