An entropy correction method for unsteady full potential flows with strong shocks

An entropy correction method for the unsteady full potential equation is presented. The unsteady potential equation is modified to account for entropy jumps across shock waves. The conservative form of the modified equation is solved in generalized coordinates using an implicit, approximate factorization method. A flux-biasing differencing method, which generates the proper amounts of artificial viscosity in supersonic regions, is used to discretize the flow equations in space. Comparisons between the present method and solutions of the Euler equations and between the present method and experimental data are presented. The comparisons show that the present method more accurately models solutions of the Euler equations and experiment than does the isentropic potential formulation

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it functional} that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerene $C_{60}$. The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system

Linear stability analysis of capillary instabilities for concentric cylindrical shells

Motivated by complex multi-fluid geometries currently being explored in fibre-device manufacturing, we study capillary instabilities in concentric cylindrical flows of $N$ fluids with arbitrary viscosities, thicknesses, densities, and surface tensions in both the Stokes regime and for the full Navier--Stokes problem. Generalizing previous work by Tomotika (N=2), Stone & Brenner (N=3, equal viscosities) and others, we present a full linear stability analysis of the growth modes and rates, reducing the system to a linear generalized eigenproblem in the Stokes case. Furthermore, we demonstrate by Plateau-style geometrical arguments that only axisymmetric instabilities need be considered. We show that the N=3 case is already sufficient to obtain several interesting phenomena: limiting cases of thin shells or low shell viscosity that reduce to N=2 problems, and a system with competing breakup processes at very different length scales. The latter is demonstrated with full 3-dimensional Stokes-flow simulations. Many $N > 3$ cases remain to be explored, and as a first step we discuss two illustrative $N \to \infty$ cases, an alternating-layer structure and a geometry with a continuously varying viscosity

Dewetting-controlled binding of ligands to hydrophobic pockets

We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly solvated pocket. The transitions lead to bimodal solvent fluctuations which govern magnitude and range of the pocket-ligand attraction. A recently developed implicit water model, based on the minimization of a geometric functional, captures the sensitive aqueous interface response to the concave-convex pocket-ligand configuration semi-quantitatively

A Replica Inference Approach to Unsupervised Multi-Scale Image Segmentation

We apply a replica inference based Potts model method to unsupervised image segmentation on multiple scales. This approach was inspired by the statistical mechanics problem of "community detection" and its phase diagram. Specifically, the problem is cast as identifying tightly bound clusters ("communities" or "solutes") against a background or "solvent". Within our multiresolution approach, we compute information theory based correlations among multiple solutions ("replicas") of the same graph over a range of resolutions. Significant multiresolution structures are identified by replica correlations as manifest in information theory overlaps. With the aid of these correlations as well as thermodynamic measures, the phase diagram of the corresponding Potts model is analyzed both at zero and finite temperatures. Optimal parameters corresponding to a sensible unsupervised segmentation correspond to the "easy phase" of the Potts model. Our algorithm is fast and shown to be at least as accurate as the best algorithms to date and to be especially suited to the detection of camouflaged images.Comment: 26 pages, 22 figure

Extended Smoothed Boundary Method for Solving Partial Differential Equations with General Boundary Conditions on Complex Boundaries

In this article, we describe an approach for solving partial differential equations with general boundary conditions imposed on arbitrarily shaped boundaries. A continuous function, the domain parameter, is used to modify the original differential equations such that the equations are solved in the region where a domain parameter takes a specified value while boundary conditions are imposed on the region where the value of the domain parameter varies smoothly across a short distance. The mathematical derivations are straightforward and generically applicable to a wide variety of partial differential equations. To demonstrate the general applicability of the approach, we provide four examples herein: (1) the diffusion equation with both Neumann and Dirichlet boundary conditions; (2) the diffusion equation with both surface diffusion and reaction; (3) the mechanical equilibrium equation; and (4) the equation for phase transformation with the presence of additional boundaries. The solutions for several of these cases are validated against corresponding analytical and semi-analytical solutions. The potential of the approach is demonstrated with five applications: surface-reaction-diffusion kinetics with a complex geometry, Kirkendall-effect-induced deformation, thermal stress in a complex geometry, phase transformations affected by substrate surfaces, and a self-propelled droplet.Comment: This document is the revised version of arXiv:0912.1288v

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

Generic Tracking of Multiple Apparent Horizons with Level Flow

We report the development of the first apparent horizon locator capable of finding multiple apparent horizons in a ``generic'' numerical black hole spacetime. We use a level-flow method which, starting from a single arbitrary initial trial surface, can undergo topology changes as it flows towards disjoint apparent horizons if they are present. The level flow method has two advantages: 1) The solution is independent of changes in the initial guess and 2) The solution can have multiple components. We illustrate our method of locating apparent horizons by tracking horizon components in a short Kerr-Schild binary black hole grazing collision.Comment: 13 pages including figures, submitted to Phys Rev