MIBPB

MaRDI QIDQ20120swMATHFDO

Official website http://www.math.msu.edu/~wei/MIBPB/

Cited in

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• NanoShaper
• ISIM
• AMBER
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• A new weak Galerkin finite element method for elliptic interface problems
• An interface-fitted mesh generator and virtual element methods for elliptic interface problems
• Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• A relaxed weak Galerkin method for elliptic interface problems with low regularity
• APBS
• CHARMM
• Delphi
• UHBD
• A new primal-dual weak Galerkin method for elliptic interface problems with low regularity assumptions
• An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
• AFMPB
• FFTSVD
• Discontinuous bubble immersed finite element method for Poisson-Boltzmann-Nernst-Planck model
• Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
• Efficient calculation of fully resolved electrostatics around large biomolecules
• Computing electrostatic binding energy with the TABI Poisson-Boltzmann solver
• Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization
• The de Rham-Hodge analysis and modeling of biomolecules
• A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule
• A meshless finite difference method for elliptic interface problems based on pivoted QR decomposition
• MIB Galerkin method for elliptic interface problems
• A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
• Interpolating stabilized moving least squares (MLS) approximation for 2D elliptic interface problems
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
• A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
• Matched interface and boundary method for elasticity interface problems
• Finite volume formulation of the MIB method for elliptic interface problems
• A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
• A Galerkin formulation of the MIB method for three dimensional elliptic interface problems
• PDB2PQR
• MCCE2
• PDB_Hydro
• TMSmesh
• A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
• IIMPACK
• BIEPACK
• PAFMPB
• High-order fractional partial differential equation transform for molecular surface construction
• Progress in developing Poisson-Boltzmann equation solvers
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding
• PoPMuSiC
• Biomolecular surface construction by PDE transform
• AQUASOL
• Quantum dynamics in continuum for proton transport. II: Variational solvent-solute interface
• DOMpro
• PBEQ-Solver
• Profunc
• UProC
• SDPBS
• DelPhi Web Server
• PyGBe
• TOMOBFLOW
• TABI
• SG
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• A topological approach for protein classification
• FreeSASA
• SAWTED
• HexServer
• PAComplex
• FoldX
• PUDGE
• SIB-BLAST
• Weak Galerkin methods for second order elliptic interface problems
• Apbsmem
• Geometric and electrostatic modeling using molecular rigidity functions
• Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
• A new Poisson-Nernst-Planck model with ion-water interactions for charge transport in ion channels
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• Multiscale geometric modeling of macromolecules. I: Cartesian representation
• Impact of geometric, thermal and tunneling effects on nano-transistors
• Second order method for solving 3D elasticity equations with complex interfaces
• SMPBS
• ESES
• ReebHanTun
• Adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients
• Lis
• DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes
• DelPhiForce
• New finite element iterative methods for solving a nonuniform ionic size modified Poisson-Boltzmann equation
• DelPhiPKa
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
• Variational multiscale models for charge transport
• A radial basis function meshless numerical method for solving interface problems in irregular domains
• Accurate p\(K_a\) computation using matched interface and boundary (MIB) method based Poisson-Boltzmann solver
• DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
• MIB method for elliptic equations with multi-material interfaces
• Second-order Poisson-Nernst-Planck solver for ion transport
• DAFMPB
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules

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