Parking functions, labeled trees and DCJ sorting scenarios

In genome rearrangement theory, one of the elusive questions raised in recent years is the enumeration of rearrangement scenarios between two genomes. This problem is related to the uniform generation of rearrangement scenarios, and the derivation of tests of statistical significance of the properties of these scenarios. Here we give an exact formula for the number of double-cut-and-join (DCJ) rearrangement scenarios of co-tailed genomes. We also construct effective bijections between the set of scenarios that sort a cycle and well studied combinatorial objects such as parking functions and labeled trees.Comment: 12 pages, 3 figure

Nonlinear nonlocal multicontinua upscaling framework and its applications

In this paper, we discuss multiscale methods for nonlinear problems. The main idea of these approaches is to use local constraints and solve problems in oversampled regions for constructing macroscopic equations. These techniques are intended for problems without scale separation and high contrast, which often occur in applications. For linear problems, the local solutions with constraints are used as basis functions. This technique is called Constraint Energy Minimizing Generalized Multiscale Finite Element Method (CEM-GMsFEM). GMsFEM identifies macroscopic quantities based on rigorous analysis. In corresponding upscaling methods, the multiscale basis functions are selected such that the degrees of freedom have physical meanings, such as averages of the solution on each continuum. This paper extends the linear concepts to nonlinear problems, where the local problems are nonlinear. The main concept consists of: (1) identifying macroscopic quantities; (2) constructing appropriate oversampled local problems with coarse-grid constraints; (3) formulating macroscopic equations. We consider two types of approaches. In the first approach, the solutions of local problems are used as basis functions (in a linear fashion) to solve nonlinear problems. This approach is simple to implement; however, it lacks the nonlinear interpolation, which we present in our second approach. In this approach, the local solutions are used as a nonlinear forward map from local averages (constraints) of the solution in oversampling region. This local fine-grid solution is further used to formulate the coarse-grid problem. Both approaches are discussed on several examples and applied to single-phase and two-phase flow problems, which are challenging because of convection-dominated nature of the concentration equation

Exploring Fijian high school students’ conceptions of averages

This paper focuses on part of a much larger study that explored form five (14 to 16 year-old) students’ ideas in statistics. A range of ideas was explored, including the students’ ideas about measures of centre and graphical representations. Students’ ideas about measures of centre were analysed and categories of responses identified. While students could compute mean and median, they were less competent with tasks that involved constructing meanings for averages. This could be due to an emphasis in the classroom on developing procedural knowledge or to linguistic and contextual problems. Some students used strategies based on prior school and everyday experiences. The paper concludes by suggesting some implications for mathematics education

Fast, adaptive, high order accurate discretization of the Lippmann-Schwinger equation in two dimension

We present a fast direct solver for two dimensional scattering problems, where an incident wave impinges on a penetrable medium with compact support. We represent the scattered field using a volume potential whose kernel is the outgoing Green's function for the exterior domain. Inserting this representation into the governing partial differential equation, we obtain an integral equation of the Lippmann-Schwinger type. The principal contribution here is the development of an automatically adaptive, high-order accurate discretization based on a quad tree data structure which provides rapid access to arbitrary elements of the discretized system matrix. This permits the straightforward application of state-of-the-art algorithms for constructing compressed versions of the solution operator. These solvers typically require $O(N^{3/2})$ work, where $N$ denotes the number of degrees of freedom. We demonstrate the performance of the method for a variety of problems in both the low and high frequency regimes.Comment: 18 page

A numerical method for junctions in networks of shallow-water channels

There is growing interest in developing mathematical models and appropriate numerical methods for problems involving networks formed by, essentially, one-dimensional (1D) domains joined by junctions. Examples include hyperbolic equations in networks of gas tubes, water channels and vessel networks for blood and lymph in the human circulatory system. A key point in designing numerical methods for such applications is the treatment of junctions, i.e. points at which two or more 1D domains converge and where the flow exhibits multidimensional behaviour. This paper focuses on the design of methods for networks of water channels. Our methods adopt the finite volume approach to make full use of the two-dimensional shallow water equations on the true physical domain, locally at junctions, while solving the usual one-dimensional shallow water equations away from the junctions. In addition to mass conservation, our methods enforce conservation of momentum at junctions; the latter seems to be the missing element in methods currently available. Apart from simplicity and robustness, the salient feature of the proposed methods is their ability to successfully deal with transcritical and supercritical flows at junctions, a property not enjoyed by existing published methodologies. Systematic assessment of the proposed methods for a variety of flow configurations is carried out. The methods are directly applicable to other systems, provided the multidimensional versions of the 1D equations are available