Finite amplitude electroconvection induced by strong unipolar injection between two coaxial cylinders

We perform a theoretical and numerical study of the Coulomb-driven electroconvection flow of a dielectric liquid between two coaxial cylinders. The specific case where the inner to outer diameter ratio is 0.5 is analyzed. A strong unipolar injection of ions either from the inner or outer cylinder is considered to introduce free charger carriers into the system. A finite volume method is used to solve all governing equations including Navier-Stokes equations and a simplified set of Maxwell’s equations. The flow is characterized by a subcritical bifurcation in the finite amplitude regime. A linear stability criterion and a nonlinear one that correspond to the onset and stop of the flow motion, respectively, are linked with a hysteresis loop. In addition, we also explore the behavior of the system for higher values of the stability parameter. For inner injection, we observe a transition between the patterns made of 7 and 8 pairs of cells, before an oscillatory regime is attained. Such a transition leads to a second finite amplitude stability criterion. A simple modal analysis reveals that the competition of different modes is at the origin of this behavior. The charge density as well as velocity field distributions are provided to help understanding the bifurcation behavior.Ministerio de ciencia y tecnología FIS2011-25161Junta de Andalucía P10-FQM-5735Junta de Andalucía P09-FQM-458

Linear stability analysis of an insoluble surfactant monolayer spreading on a thin liquid film

Recent experiments by several groups have uncovered a novel fingering instability in the spreading of surface active material on a thin liquid film. The mechanism responsible for this instability is yet to be determined. In an effort to understand this phenomenon and isolate a possible mechanism, we have investigated the linear stability of a coupled set of equations describing the Marangoni spreading of a surfactant monolayer on a thin liquid support. The unperturbed flows, which exhibit simple linear behavior in the film thickness and surfactant concentration, are self-similar solutions of the first kind for spreading in a rectilinear geometry. The solution of the disturbance equations determines that the rectilinear base flows are linearly stable. An energy analysis reveals why these base flows can successfully heal perturbations of all wavenumbers. The details of this analysis suggest, however, a mechanism by which the spreading can be destabilized. We propose how the inclusion of additional forces acting on the surfactant coated spreading film might give rise to regions of adverse mobility gradients known to produce fingering instabilities in other fluid flows

Introduction to the Special Issue on Partial Differential Equations and Geometry-Driven Diffusion in Image Processing and Analysis

©1998 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.DOI: 10.1109/TIP.1998.66117

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Reaction-diffusion dynamics: confrontation between theory and experiment in a microfluidic reactor

We confront, quantitatively, the theoretical description of the reaction-diffusion of a second order reaction to experiment. The reaction at work is \ca/CaGreen, and the reactor is a T-shaped microchannel, 10 $\mu$m deep, 200 $\mu$m wide, and 2 cm long. The experimental measurements are compared with the two-dimensional numerical simulation of the reaction-diffusion equations. We find good agreement between theory and experiment. From this study, one may propose a method of measurement of various quantities, such as the kinetic rate of the reaction, in conditions yet inaccessible to conventional methods

Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces

In this paper we present computational techniques to investigate the solutions of two-component, nonlinear reaction-diffusion (RD) systems on arbitrary surfaces. We build on standard techniques for linear and nonlinear analysis of RD systems, and extend them to operate on large-scale meshes for arbitrary surfaces. In particular, we use spectral techniques for a linear stability analysis to characterize and directly compose patterns emerging from homogeneities. We develop an implementation using surface finite element methods and a numerical eigenanalysis of the Laplace-Beltrami operator on surface meshes. In addition, we describe a technique to explore solutions of the nonlinear RD equations using numerical continuation. Here, we present a multiresolution approach that allows us to trace solution branches of the nonlinear equations efficiently even for large-scale meshes. Finally, we demonstrate the working of our framework for two RD systems with applications in biological pattern formation: a Brusselator model that has been used to model pattern development on growing plant tips, and a chemotactic model for the formation of skin pigmentation patterns. While these models have been used previously on simple geometries, our framework allows us to study the impact of arbitrary geometries on emerging patterns.Comment: This paper was submitted at the Journal of Mathematical Biology, Springer on 07th July 2015, in its current form (barring image references on the last page and cosmetic changes owning to rebuild for arXiv). The complete body of work presented here was included and defended as a part of my PhD thesis in Nov 2015 at the University of Ber

Strain localization in a shear transformation zone model for amorphous solids

We model a sheared disordered solid using the theory of Shear Transformation Zones (STZs). In this mean-field continuum model the density of zones is governed by an effective temperature that approaches a steady state value as energy is dissipated. We compare the STZ model to simulations by Shi, et al.(Phys. Rev. Lett. 98 185505 2007), finding that the model generates solutions that fit the data,exhibit strain localization, and capture important features of the localization process. We show that perturbations to the effective temperature grow due to an instability in the transient dynamics, but unstable systems do not always develop shear bands. Nonlinear energy dissipation processes interact with perturbation growth to determine whether a material exhibits strain localization. By estimating the effects of these interactions, we derive a criterion that determines which materials exhibit shear bands based on the initial conditions alone. We also show that the shear band width is not set by an inherent diffusion length scale but instead by a dynamical scale that depends on the imposed strain rate.Comment: 8 figures, references added, typos correcte

Analysis of plasma instabilities and verification of the BOUT code for the Large Plasma Device

The properties of linear instabilities in the Large Plasma Device [W. Gekelman et al., Rev. Sci. Inst., 62, 2875 (1991)] are studied both through analytic calculations and solving numerically a system of linearized collisional plasma fluid equations using the 3D fluid code BOUT [M. Umansky et al., Contrib. Plasma Phys. 180, 887 (2009)], which has been successfully modified to treat cylindrical geometry. Instability drive from plasma pressure gradients and flows is considered, focusing on resistive drift waves, the Kelvin-Helmholtz and rotational interchange instabilities. A general linear dispersion relation for partially ionized collisional plasmas including these modes is derived and analyzed. For LAPD relevant profiles including strongly driven flows it is found that all three modes can have comparable growth rates and frequencies. Detailed comparison with solutions of the analytic dispersion relation demonstrates that BOUT accurately reproduces all characteristics of linear modes in this system.Comment: Published in Physics of Plasmas, 17, 102107 (2010

Partial differential equations for self-organization in cellular and developmental biology

Understanding the mechanisms governing and regulating the emergence of structure and heterogeneity within cellular systems, such as the developing embryo, represents a multiscale challenge typifying current integrative biology research, namely, explaining the macroscale behaviour of a system from microscale dynamics. This review will focus upon modelling how cell-based dynamics orchestrate the emergence of higher level structure. After surveying representative biological examples and the models used to describe them, we will assess how developments at the scale of molecular biology have impacted on current theoretical frameworks, and the new modelling opportunities that are emerging as a result. We shall restrict our survey of mathematical approaches to partial differential equations and the tools required for their analysis. We will discuss the gap between the modelling abstraction and biological reality, the challenges this presents and highlight some open problems in the field