Differential geometry based multiscale models
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Publication:711499
DOI10.1007/s11538-010-9511-xzbMath1198.92001OpenAlexW2086200041WikidataQ42589738 ScholiaQ42589738MaRDI QIDQ711499
Publication date: 26 October 2010
Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/s11538-010-9511-x
elasticityvariational principleNavier-Stokes equationmolecular dynamicsPoisson-Boltzmann equationgeometric flowsNernst-Planck equationelectrostatic analysisimplicit solvent modelssolvation analysis
Biophysics (92C05) Applications of local differential geometry to the sciences (53B50) General biology and biomathematics (92B05)
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Cites Work
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Nonlinear total variation based noise removal algorithms
- A numerical method for computing minimal surfaces in arbitrary dimension
- Differential geometry based solvation model. I: Eulerian formulation
- The WKB local discontinuous Galerkin method for the simulation of Schrödinger equation in a resonant tunneling diode
- Discrete singular convolution-finite subdomain method for the solution of incompressible viscous flows
- Motion of level sets by mean curvature. I
- Geometric and potential driving formation and evolution of biomolecular surfaces
- On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method
- Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces
- Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations
- Numerical analysis of blood flow in the heart
- Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
- Geodesic active contours
- High resolution conjugate filters for the simulation of flows.
- Semi-implicit level set methods for curvature and surface diffusion motion
- Image sharpening by flows based on triple well potentials
- \(H^ 1\) solutions of a class of fourth order nonlinear equations for image processing.
- A high-order discontinuous Galerkin method for 2D incompressible flows
- Shock capturing by anisotropic diffusion oscillation reduction
- Subjective surfaces: A geometric model for boundary completion
- 3D curves reconstruction based on deformable models
- A phase field approach in the numerical study of the elastic bending energy for vesicle membranes
- High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces
- Computing minimal surfaces via level set curvature flow
- Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities
- A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces
- A windowed Fourier pseudospectral method for hyperbolic conservation laws
- High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
- A pseudo-spectral multiscale method: interfacial conditions and coarse grid equations
- Quality meshing of implicit solvation models of biomolecular structures
- Discrete surface modelling using partial differential equations
- VIBRATION ANALYSIS BY DISCRETE SINGULAR CONVOLUTION
- Optimal approximations by piecewise smooth functions and associated variational problems
- Feature-Oriented Image Enhancement Using Shock Filters
- Curvature Measures
- Noise removal using fourth-order partial differential equation with applications to medical magnetic resonance images in space and time
- PEM Fuel Cells: A Mathematical Overview
- A Critical Overview of Computational Fluid Dynamics Multiphase Models for Proton Exchange Membrane Fuel Cells
- Asymptotic Expansions of I-V Relations via a Poisson–Nernst–Planck System
- Computing Discrete Minimal Surfaces and Their Conjugates
- A general framework for low level vision
- Traveling Wave Solutions of Fourth Order PDEs for Image Processing
- Low‐curvature image simplifiers: Global regularity of smooth solutions and Laplacian limiting schemes
- Discrete singular convolution and its application to the analysis of plates with internal supports. Part 1: Theory and algorithm
- A direct method for solving an anisotropic mean curvature flow of plane curves with an external force
- Large-scale molecular dynamics simulations of normal shock waves in dilute argon
- A new algorithm for solving some mechanical problems
- Evolution, implementation, and application of level set and fast marching methods for advancing fronts
- An analysis of the quasicontinuum method