We perform a numerical study of the fluctuations of the rescaled hydrodynamic transversevelocity field during the cooling state of a homogeneous granular gas. We are interestedin the role of Molecular Chaos for the amplitude of the hydrodynamic noise and itsrelaxation in time. For this purpose we compare the results of Molecular Dynamics (MD,deterministic dynamics) with those from Direct Simulation Monte Carlo (DSMC, randomprocess), where Molecular Chaos can be directly controlled. It is seen that the large timedecay of the fluctuation’s autocorrelation is always dictated by the viscosity coefficientpredicted by granular hydrodynamics, independently of the numerical scheme (MD or DSMC).On the other side, the noise amplitude in Molecular Dynamics, which is known toviolate the equilibrium Fluctuation-Dissipation relation, is not alwaysaccurately reproduced in a DSMC scheme. The agreement between the two models improves ifthe probability of recollision (controlling Molecular Chaos) is reduced by increasing thenumber of virtual particles per cells in the DSMC. This result suggests that DSMC is notnecessarily more efficient than MD, if the real number of particles is small(~103 ± 104) and if one is interested in accurately reproducefluctuations. An open question remains about the small-times behavior of theautocorrelation function in the DSMC, which in MD and in kinetic theory predictions is nota straight exponential.

Continuum mechanics (e.g., hydrodynamics, elasticity theory) is based on the assumptionthat a small set of fields provides a closed description on large space and time scales.Conditions governing the choice for these fields are discussed in the context of granularfluids and multi-component fluids. In the first case, the relevance of temperature orenergy as a hydrodynamic field is justified. For mixtures, the use of a total temperatureand single flow velocity is compared with the use of multiple species temperatures andvelocities.

Compartmentalization is a general principle in biological systems which is observable on all size scales, ranging from organelles inside of cells, cells in histology, and up to the level of groups, herds, swarms, meta-populations, and populations. Compartmental models are often used to model such phenomena, but such models can be both highly nonlinear and difficult to work with.

Fortunately, there are many significant biological systems that are amenable to linear compartmental models which are often more mathematically accessible. Moreover, the biology and mathematics is often so intertwined in such models that one can be used to better understand the other. Indeed, as we demonstrate in this paper, linear compartmental models of migratory dynamics can be used as an exciting and interactive means of introducing sophisticated mathematics, and conversely, the associated mathematics can be used to demonstrate important biological properties not only of seasonal migrations but also of compartmental models in general.

We have found this approach to be of great value in introducing derivatives, integrals, and the fundamental theorem of calculus. Additionally, these models are appropriate as applications in a differential equations course, and they can also be used to illustrate important ideas in probability and statistics, such as the Poisson distribution.

Various particle methods are widely used to model dynamics of complex media. In this workmolecular dynamics and dissipative particles dynamics are applied to model blood flowscomposed of plasma and erythrocytes. The properties of the homogeneous particle fluid arestudied. Capillary flows with erythrocytes are investigated.

Blood rheology is completely determined by its major corpuscles which are erythrocytes,or red blood cells (RBCs). That is why understanding and correct mathematical descriptionof RBCs behavior in blood is a critical step in modelling the blood dynamics. Variousphenomena provided by RBCs such as aggregation, deformation, shear-induced diffusion andnon-uniform radial distribution affect the passage of blood through the vessels. Hence,they have to be taken into account while modelling the blood dynamics. Other importantblood corpuscles are platelets, which are crucial for blood clotting. RBCs strongly affectthe platelet transport in blood expelling them to the vessel walls and increasing theirdispersion, which has to be considered in models of clotting. In this article we give abrief review of basic modern approaches in mathematical description of these phenomena,discuss their applicability to real flow conditions and propose further pathways fordeveloping the theory of blood flow.

We propose a mixed formulation for non-isothermal Oldroyd–Stokes problem where the bothextra stress and the heat flux’s vector are considered. Based on such a formulation, adual mixed finite element is constructed and analyzed. This finite element method enablesus to obtain precise approximations of the dual variable which are, for the non-isothermalfluid flow problems, the viscous and polymeric components of the extra-stress tensor, aswell as the heat flux. Furthermore, it has properties analogous to the finite volumemethods, namely, the local conservation of the momentum and the mass.

This paper deals with the evolution Fokker-Planck-Smoluchowski configurationalprobability diffusion equation for the FENE dumbbell model in dilute polymer solutions. Weprove the exponential convergence in time of the solution of this equation to acorresponding steady-state solution, for arbitrary velocity gradients.

Caused by the problem of unilateral contact during vibrations of satellite solar arrays, the aim of this paper is to better understand such a phenomenon. Therefore, it is studied here a simplified model composed by a beam moving between rigid obstacles. Our purpose is to describe and compare some families of fully discretized approximations and their properties, in the case of non-penetration Signorini's conditions. For this, starting from the works of Dumont and Paoli, we adapt to our beam model the singular dynamic method introduced by Renard. A particular emphasis is given in the use of a restitution coefficient in the impact law. Finally, various numerical results are presented and energy conservation capabilities of the schemes are investigated.

A mathematical model of infiltrative tumour growth is investigated taking into account transitions between two possible states of malignant cells: proliferation and migration. These transitions are considered to depend on oxygen level in a threshold manner where high oxygen concentration allows cell proliferation, while concentration below a certain critical value induces cell migration. The infiltrative tumour spreading rate dependence on model parameters is obtained. It is shown that the tumour growth rate depends on the tissue oxygen level in a threshold manner.

There is a growing interest in high-order finite and spectral/hp elementmethods using continuous and discontinuous Galerkin formulations. In this paper weinvestigate the effect of h- and p-type refinement onthe relationship between runtime performance and solution accuracy. The broad spectrum ofpossible domain discretisations makes establishing a performance-optimal selectionnon-trivial. Through comparing the runtime of different implementations for evaluatingoperators over the space of discretisations with a desired solution tolerance, wedemonstrate how the optimal discretisation and operator implementation may be selected fora specified problem. Furthermore, this demonstrates the need for codes to support bothlow- and high-order discretisations.

A growing body of literature testifies to the importance of quantitative reasoning skillsin the 21st-century biology curriculum, and to the learning benefits associated withactive pedagogies. The process of modeling a biological system provides an approach thatintegrates mathematical skills and higher-order thinking with existing course contentknowledge. We describe a general strategy for teaching model-building in an introductorybiology course, using the example of a model of an infectious disease outbreak.Preliminary assessment data suggest that working through the formal process of modelconstruction may help students develop their scientific reasoning and communicationskills.

Infectious diseases ranging from the common cold to cholera affect our society physically, emotionally, ecologically, and economically. Yet despite their importance and impact, there remains a lack of effective teaching materials for epidemiology and disease ecology in K-12, undergraduate, and graduate curricula [2]. To address this deficit, we’ve developed a classroom lesson with three instructional goals: (1) Familiarize students on basic concepts of infectious disease ecology; (2) Introduce students to a classic compartmental model and its applications in epidemiology; (3) Demonstrate the application and importance of mathematical modeling as a tool in biology. The instructional strategy uses a game-based mathematical manipulative designed to engage students in the concepts of infectious disease spread. It has the potential to be modified for target audiences ranging from Kindergarten to professional schools in science, public health, policy, medical, and veterinarian programs. In addition, we’ve provided variations of the activity to enhance the transfer of fundamental concepts covered in the initial lesson to more complex concepts associated with vaccination and waning immunity. While 10 variations are presented here, the true number of directions in which the game might extend will only be limited by the imagination of its students [6].

Peristaltic pumping of fluid is a fundamental method of transport in many biologicalprocesses. In some instances, particles of appreciable size are transported along with thefluid, such as ovum transport in the oviduct or kidney stones in the ureter. In some ofthese biological settings, the fluid may be viscoelastic. In such a case, a nonlinearconstitutive equation to describe the evolution of the viscoelastic contribution to thestress tensor must be included in the governing equations. Here we use an immersedboundary framework to study peristaltic transport of a macroscopic solid particle in aviscoelastic fluid governed by a Navier-Stokes/Oldroyd-B model. Numerical simulations ofperistaltic pumping as a function of Weissenberg number are presented. We examine thespatial and temporal evolution of the polymer stress field, and also find that theviscoelasticity of the fluid does hamper the overall transport of the particle in thedirection of the wave.

An analysis of all possible icosahedral viral capsids is proposed. It takes into accountthe diversity of coat proteins and their positioning in elementary pentagonal andhexagonal configurations, leading to definite capsid size. We show that theself-organization of observed capsids during their production implies a definitecomposition and configuration of elementary building blocks. The exact number of differentprotein dimers is related to the size of a given capsid, labeled by itsT-number. Simple rules determining these numbers for each value ofT are deduced and certain consequences concerning the probabilities ofmutations and evolution of capsid viruses are discussed.

The newly developed unifying discontinuous formulation named the correction procedure viareconstruction (CPR) for conservation laws is extended to solve the Navier-Stokesequations for 3D mixed grids. In the current development, tetrahedrons and triangularprisms are considered. The CPR method can unify several popular high order methodsincluding the discontinuous Galerkin and the spectral volume methods into a more efficientdifferential form. By selecting the solution points to coincide with the flux points,solution reconstruction can be completely avoided. Accuracy studies confirmed that theoptimal order of accuracy can be achieved with the method. Several benchmark test casesare computed by solving the Euler and compressible Navier-Stokes equations to demonstrateits performance.

In this paper we build and analyze networks using the statistical and programmingenvironment R and the igraph package. We investigate random, small-world, and scale-freenetworks and test a standard problem of connectivity on a random graph. We then develop amethod to study how vaccination can alter the structure of a disease transmission network.We also discuss a variety of other uses for networks in biology.

Over the last three decades Computational Fluid Dynamics (CFD) has gradually joined thewind tunnel and flight test as a primary flow analysis tool for aerodynamic designers. CFDhas had its most favorable impact on the aerodynamic design of the high-speed cruiseconfiguration of a transport. This success has raised expectations among aerodynamiciststhat the applicability of CFD can be extended to the full flight envelope. However, thecomplex nature of the flows and geometries involved places substantially increased demandson the solution methodology and resources required. Currently most simulations involveReynolds-Averaged Navier-Stokes (RANS) codes although Large Eddy Simulation (LES) andDetached Eddy Suimulation (DES) codes are occasionally used for component analysis ortheoretical studies. Despite simplified underlying assumptions, current RANS turbulencemodels have been spectacularly successful for analyzing attached, transonic flows. Whetheror not these same models are applicable to complex flows with smooth surface separation isan open question. A prerequisite for answering this question is absolute confidence thatthe CFD codes employed reliably solve the continuous equations involved. Too often,failure to agree with experiment is mistakenly ascribed to the turbulence model ratherthan inadequate numerics. Grid convergence in three dimensions is rarely achieved. Evenresidual convergence on a given grid is often inadequate. This paper discusses issuesinvolved in residual and especially grid convergence.

A finite volume method for the simulation of compressible aerodynamic flows is described.Stabilisation and shock capturing is achieved by the use of an HLLC consistent numericalflux function, with acoustic wave improvement. The method is implemented on anunstructured hybrid mesh in three dimensions. A solution of higher order accuracy isobtained by reconstruction, using an iteratively corrected least squares process, and by anew limiting procedure. The numerical performance of the complete approach is demonstratedby considering its application to the simulation of steady turbulent transonic flow overan ONERA M6 wing and to a steady inviscid supersonic flow over a modern military aircraftconfiguration.

This paper is devoted to solving of dynamic problems in biomechanics that requiredetailed study of fast processes. Numerical method of characteristics is used to model thetemporal development of the processes with high accuracy.