Exhibiting cross-diffusion-induced patterns for reaction-diffusion systems on evolving domains and surfaces

The aim of this manuscript is to present for the first time the application of the finite element method for solving reaction-diffusion systems with cross-diffusion on continuously evolving domains and surfaces. Furthermore we present pattern formation generated by the reaction-diffusion systemwith cross-diffusion on evolving domains and surfaces. A two-component reaction-diffusion system with linear cross-diffusion in both u and v is presented. The finite element method is based on the approximation of the domain or surface by a triangulated domain or surface consisting of a union of triangles. For surfaces, the vertices of the triangulation lie on the continuous surface. A finite element space of functions is then defined by taking the continuous functions which are linear affine on each simplex of the triangulated domain or surface. To demonstrate the role of cross-diffusion to the theory of pattern formation, we compute patterns with model kinetic parameter values that belong only to the cross-diffusion parameter space; these do not belong to the standard parameter space for classical reaction-diffusion systems. Numerical results exhibited show the robustness, flexibility, versatility, and generality of our methodology; the methodology can deal with complicated evolution laws of the domain and surface, and these include uniform isotropic and anisotropic growth profiles as well as those profiles driven by chemical concentrations residing in the domain or on the surface

Coupling nonpolar and polar solvation free energies in implicit solvent models

Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current implicit solvent models. We suggest a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy of the solvent with respect to a solvent volume exclusion function. The resulting differential equation is similar to the Laplace-Young equation for the geometrical description of capillary interfaces, but is extended to microscopic scales by explicitly considering curvature corrections as well as dispersion and electrostatic contributions. Unlike existing implicit solvent approaches, the solvent accessible surface is an output of our model. The presented formalism is illustrated on spherically or cylindrically symmetrical systems of neutral or charged solutes on different length scales. The results are in agreement with computer simulations and, most importantly, demonstrate that our method captures the strong sensitivity of solvent expulsion and dewetting to the particular form of the solvent-solute interactions.Comment: accpted in J. Chem. Phy

Two-phase viscoelastic jetting

A coupled finite difference algorithm on rectangular grids is developed for viscoelastic ink ejection simulations. The ink is modeled by the Oldroyd-B viscoelastic fluid model. The coupled algorithm seamlessly incorporates several things: (1) a coupled level set-projection method for incompressible immiscible two-phase fluid flows; (2) a higher-order Godunov type algorithm for the convection terms in the momentum and level set equations; (3) a simple first-order upwind algorithm for the convection term in the viscoelastic stress equations; (4) central difference approximations for viscosity, surface tension, and upper-convected derivative terms; and (5) an equivalent circuit model to calculate the inflow pressure (or flow rate) from dynamic voltage

The Effect of Neutral Atoms on Capillary Discharge Z-pinch

We study the effect of neutral atoms on the dynamics of a capillary discharge Z-pinch, in a regime for which a large soft-x-ray amplification has been demonstrated. We extended the commonly used one-fluid magneto-hydrodynamics (MHD) model by separating out the neutral atoms as a second fluid. Numerical calculations using this extended model yield new predictions for the dynamics of the pinch collapse, and better agreement with known measured data.Comment: 4 pages, 4 postscript figures, to be published in Phys. Rev. Let

NRL capillary Z-pinch experiment

The current renewed interest in the dense linear z-pinch is due in large part to a recent Los Alamos Study which concluded that a z- pinch based reactor could produce 4.4 KJ of fusion energy per pulse for the modest input of 140 kJ per pulse, if a straight pinch could be maintained for 2 {mu}sec. Early attempts to achieve suitable high density z-pinches were of the implosion type which produced hollow pressure profiles that quickly resulted in disruptive m = 0 instabilities. These instabilities are not found in the gas embedded pinch in which an initially small diameter plasma is kept in radial equilibrium by following a prescribed current waveform. Unfortunately, these pinches are prone to a rapid accretion of the surrounding gas during the early stages of formation. Our approach is to form the pinch inside small diameter quartz capillaries filled with neutral hydrogen. This fixes the line density. By driving currents through the pinch at a rate that exceeds that necessary for radial equilibrium, we expect the pinch to contract away from the walls and be subject to compressional, as well as ohmic heating. This contraction will, of course, produce a plasma between the pinch and the capillary wall, but we anticipate this ``corona`` will be kept at a low temperature (i.e., high resistance) by radiation and hence shunt only a small fraction of the pinch current. We also expect negligible impurities in the pinch as the classical mixing time will be much longer than the pinch duration at the densities (10{sup 21}- 10{sup 22} ions/cm{sup 3}) and magnetic fields (1 - 10 MG) involved. However, we do expect the presence of the dense corona to reduce the growth rate of the m = 1 instability. Our results demonstrate that a z-pinch can be formed inside a capillary, but our limited current rise rates and peak current have limited our test abilities. Planned improvements in electrical equipment should yield successful testing results

A new ghost cell/level set method for moving boundary problems:application to tumor growth

In this paper, we present a ghost cell/level set method for the evolution of interfaces whose normal velocity depend upon the solutions of linear and nonlinear quasi-steady reaction-diffusion equations with curvature-dependent boundary conditions. Our technique includes a ghost cell method that accurately discretizes normal derivative jump boundary conditions without smearing jumps in the tangential derivative; a new iterative method for solving linear and nonlinear quasi-steady reaction-diffusion equations; an adaptive discretization to compute the curvature and normal vectors; and a new discrete approximation to the Heaviside function. We present numerical examples that demonstrate better than 1.5-order convergence for problems where traditional ghost cell methods either fail to converge or attain at best sub-linear accuracy. We apply our techniques to a model of tumor growth in complex, heterogeneous tissues that consists of a nonlinear nutrient equation and a pressure equation with geometry-dependent jump boundary conditions. We simulate the growth of glioblastoma (an aggressive brain tumor) into a large, 1 cm square of brain tissue that includes heterogeneous nutrient delivery and varied biomechanical characteristics (white matter, gray matter, cerebrospinal fluid, and bone), and we observe growth morphologies that are highly dependent upon the variations of the tissue characteristics—an effect observed in real tumor growth

Aquatics reconstruction software: the design of a diagnostic tool based on computer vision algorithms

Computer vision methods can be applied to a variety of medical and surgical applications, and many techniques and algorithms are available that can be used to recover 3D shapes and information from images range and volume data. Complex practical applications, however, are rarely approachable with a single technique, and require detailed analysis on how they can be subdivided in subtasks that are computationally treatable and that, at the same time, allow for the appropriate level of user-interaction. In this paper we show an example of a complex application where, following criteria of efficiency, reliability and user friendliness, several computer vision techniques have been selected and customized to build a system able to support diagnosis and endovascular treatment of Abdominal Aortic Aneurysms. The system reconstructs the geometrical representation of four different structures related to the aorta (vessel lumen, thrombus, calcifications and skeleton) from CT angiography data. In this way it supports the three dimensional measurements required for a careful geometrical evaluation of the vessel, that is fundamental to decide if the treatment is necessary and to perform, in this case, its planning. The system has been realized within the European trial AQUATICS (IST-1999-20226 EUTIST-M WP 12), and it has been widely tested on clinical data

Shapes of leading tunnelling trajectories for single-electron molecular ionization

Based on the geometrical approach to tunnelling by P.D. Hislop and I.M. Sigal [Memoir. AMS 78, No. 399 (1989)], we introduce the concept of a leading tunnelling trajectory. It is then proven that leading tunnelling trajectories for single-active-electron models of molecular tunnelling ionization (i.e., theories where a molecular potential is modelled by a single-electron multi-centre potential) are linear in the case of short range interactions and "almost" linear in the case of long range interactions. The results are presented on both the formal and physically intuitive levels. Physical implications of the obtained results are discussed.Comment: 14 pages, 5 figure