Basics of qualitative research: Grounded theory procedures and techniques

This paper is concerned with the mathematical structure of the immersed boundary (IB) method, which is intended for the computer simulation of fluid–structure interaction, especially in biological fluid dynamics. The IB formulation of such problems, derived here from the principle of least action, involves both Eulerian and Lagrangian variables, linked by the Dirac delta function. Spatial discretization of the IB equations is based on a fixed Cartesian mesh for the Eulerian variables, and a moving curvilinear mesh for the Lagrangian variables. The two types of variables are linked by interaction equations that involve a smoothed approximation to the Dirac delta function. Eulerian/Lagrangian identities govern the transfer of data from one mesh to the other. Temporal discretization is by a second-order Runge–Kutta method. Current and future research directions are pointed out, and applications of the IB method are briefly discussed. Introduction The immersed boundary (IB) method was introduced to study flow patterns around heart valves and has evolved into a generally useful method for problems of fluid–structure interaction. The IB method is both a mathematical formulation and a numerical scheme. The mathematical formulation employs a mixture of Eulerian and Lagrangian variables. These are related by interaction equations in which the Dirac delta function plays a prominent role. In the numerical scheme motivated by the IB formulation, the Eulerian variables are defined on a fixed Cartesian mesh, and the Lagrangian variables are defined on a curvilinear mesh that moves freely through the fixed Cartesian mesh without being constrained to adapt to it in any way at all.

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The immersed boundary method

미국의 “전국 수학 교사 협의회”(National Council of Teachers of Mathematics, NCTM)는 1989년부터 〈학교 수학의 교육과정과 평가 규준〉(1989), 〈수학 가르침(교수)의 전문성 규준〉(1991), 〈학교 수학의 평가(시험) 규준〉(NCTM, 1995), 〈학교 수학의 원리와 규준〉(2000)을 출판하여 미국의 수학 교육 의 전망(목표, 나아갈 길)과 규준(실행 지침)을 제시하였다. 수학 교사들로 구성된 미국의 NCTM은 학생, 학부모, 학교 행정가 등 많은 사람들과 힘을 합하여 모든 학생들에게 수준 높은 수학 교육을 받을 수 있는 여건(환경, 기회)을 조성하는 데 구심점의 역할을 하였다. 한편 많은 관련 단체들은 여러 배경과 능력을 가진 학생들이 전문성을 지닌 교사(특수 교사를 일컫는 밀이 아니다. 수학 교과를 이해하고 수학의 전문성과 특수성을 가르칠 수 있는 일반 교사를 일컫는 말이다.)로부터 미래를 대비해 평등하고, 진취적이며, 지원이 잘 이루어지고, 공학 도구(IT)가 잘 갖춰진 환경에서 중요한 수학적 아이디어를 이해하면서 학습할 수 있는 수학 교실(미국에서는 우리나라처럼 수학 교사가 수학 시간에 학생의 방(교실: Homeroom)에 찾아가지 않고 학생들이 선생의 방(수학 교실: Classroom)을 찾아온다. 전형적인 수학 교실의 사진은 2쪽에 나와 있다.)을 만들기 위해 함께 힘썼다. NCTM에서 출간한 여러 규준들은 우리나라의 제6차와 제7차 교육과정에도 큰 영향을 미쳤다. 이 글에서는 NCTM(2000)에서 제시한 학습 원리를 간단히 살펴본 다음 이를 중심으로 현재 미국 수학 교육의 교수ㆍ학습 이론의 동향을 살펴본다.

미국 NCTM의 Principles and Standards for School Mathematics에 나타난 수학과 교수,학습의 이론

Cell motility in viscous fluids is ubiquitous and affects many biological processes, including reproduction, infection and the marine life ecosystem. Here we review the biophysical and mechanical principles of locomotion at the small scales relevant to cell swimming, tens of micrometers and below. At this scale, inertia is unimportant and the Reynolds number is small. Our emphasis is on the simple physical picture and fundamental flow physics phenomena in this regime. We first give a brief overview of the mechanisms for swimming motility, and of the basic properties of flows at low Reynolds number, paying special attention to aspects most relevant for swimming such as resistance matrices for solid bodies, flow singularities and kinematic requirements for net translation. Then we review classical theoretical work on cell motility, in particular early calculations of swimming kinematics with prescribed stroke and the application of resistive force theory and slender-body theory to flagellar locomotion. After examining the physical means by which flagella are actuated, we outline areas of active research, including hydrodynamic interactions, biological locomotion in complex fluids, the design of small-scale artificial swimmers and the optimization of locomotion strategies. (Some figures in this article are in colour only in the electronic version) This article was invited by Christoph Schmidt.

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The hydrodynamics of swimming microorganisms

Differently from passive Brownian particles, active particles, also known as self-propelled Brownian particles or microswimmers and nanoswimmers, are capable of taking up energy from their environment and converting it into directed motion. Because of this constant flow of energy, their behavior can be explained and understood only within the framework of nonequilibrium physics. In the biological realm, many cells perform directed motion, for example, as a way to browse for nutrients or to avoid toxins. Inspired by these motile microorganisms, researchers have been developing artificial particles that feature similar swimming behaviors based on different mechanisms. These man-made micromachines and nanomachines hold a great potential as autonomous agents for health care, sustainability, and security applications. With a focus on the basic physical features of the interactions of self-propelled Brownian particles with a crowded and complex environment, this comprehensive review will provide a guided tour through its basic principles, the development of artificial self-propelling microparticles and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

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Active Particles in Complex and Crowded Environments

https://crd.lbl.gov/assets/pubs_presos/insNewSpringer.pdf

Accurate projection methods for the incompressible Navier—Stokes equations

A numerical method for computing Stokes flows in the presence of immersed boundaries and obstacles is presented. The method is based on the smoothing of the forces, leading to regularized Stokeslets. The resulting expressions provide the pressure and velocity field as functions of the forcing. The latter expression can also be inverted to find the forces that impose a given velocity boundary condition. The numerical examples presented demonstrate the wide applicability of the method and its properties. Solutions converge with second-order accuracy when forces are exerted along smooth boundaries. Examples of segmented boundaries and forcing at random points are also presented.

The Method of Regularized Stokeslets

The method of regularized Stokeslets is a Lagrangian method for computing Stokes flow driven by forces distributed at material points in a fluid. It is based on the superposition of exact solutions of the Stokes equations when forces are given by a cutoff function. We present this method in three dimensions, along with an analysis of its accuracy and performance on the model problems of flow past a sphere and the steady state rotation of rigid helical tubes. Predicted swimming speeds for various helical geometries are compared with experimental data for motile spirochetes. In addition, the regularized Stokeslet method is readily implemented in conjunction with an immersed boundary representation of an elastic helix that incorporates passive elastic properties as well as mechanisms of internal force generation.

The method of regularized Stokeslets in three dimensions : Analysis, validation, and application to helical swimming

Nearly close-packed populations of the swimming bacterium Bacillus subtilis form a collective phase, the “Zooming BioNematic” (ZBN). This state exhibits large-scale orientational coherence, analogous to the molecular alignment of nematic liquid crystals, coupled with remarkable spatial and temporal correlations of velocity and vorticity, as measured by both novel and standard applications of particle imaging velocimetry. The appearance of turbulent dynamics in a system which is nominally in the regime of Stokes flow can be understood by accounting for the local energy input by the swimmers, with a new dimensionless ratio analogous to the Reynolds number. The interaction between organisms and boundaries, and with one another, is modeled by application of the methods of regularized Stokeslets.

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Ricardo Cortez

Papers

Accurate projection methods for the incompressible Navier—Stokes equations

The Method of Regularized Stokeslets

The method of regularized Stokeslets in three dimensions : Analysis, validation, and application to helical swimming

Fluid dynamics of self-propelled microorganisms, from individuals to concentrated populations

The method of images for regularized Stokeslets