Computational Electrostatics for Biological Applications

ELECTROSTATICS and CONTINUUM SOLVENT MODELS

Electrostatics models for Biology
Classical density functional theories of ionic solutions

Introducing charge hydration asymmetry into continuum electrostatics framework


NUMERICAL APPROACHES AND SOLVERS
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Continuum electrostatics for Biological Applications: the DelPhi case
Discontinuous Galerkin schemes for elliptic problems.

Surface Electrostatics Using An Adaptive Cartesian Grid-Based Poisson-Boltzmann Solver

Design, Development and Applications of the MEAD Suite for Macromolecular Electrostatics

Progress and Challenges in Boundary-Integral Methods for Biological Electrostatics

Efficient Boundary Element Method with curved elements for implicit solvation in biological systems

Generalized Born forces: surface integral formulation.

MOLECULAR SURFACE MODELS

Molecular surface design with balls

State-of-the-art and perspectives of implicit modeling for molecular surfaces

A Generic Framework for Delaunay Mesh Generation and Optimization

BROADENING THE VIEW
Multiscale multiphysics and multidomain models for biomolecular systems

Beyond computation, the representation of electrostatics in biological settings

DEALING WITH COMPUTATIONAL COMPLEXITY
NanoShaper: a general and robust ray-casting based tool for processing surfaces at the nanoscale

Triangulating Molecular Surfaces with Millions of Atoms

Mixed MPI/CUDAimplementation for PB equation

APPLICATIONS TO BIOLOGY AND BIOPHYSICS

Control of DNA Minor Groove Width and Electrostatic Potential in Fis Binding Sequences

Computing protein binding properties from molecular electrostatic potentials

Comparative Poisson-Boltzmann equation calculations for binding free energies focusing on physical and algorithmic parameters

Biophysical Applications of the Adaptive Cartesian Grid Poisson-Boltzmann Equation Software Package

Structural and electrostaticdeterminants of interaction specificity in G-protein mediated signaling

Using structural and physical-chemical parameters to identify functional districts in proteins - the role of electrostatic potential

A Molecular Dynamics (MD) insight to the electrostatics of biological (lipid) bilayers. A tool for understanding electroporation mechanisms

Modeling protein-ligand interaction with finite absorbing Markov chain

Molecular Mechanics - Poisson Boltzmann Surface Area calculations using AMBER program package - application to the human dipeptidyl petidase III

Long range Debye-Huckel correction for computation of grid-based electrostatic forces between biomacromolecules

APPLICATIONS TO NANOTECHNOLOGY
Modeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticle

Modelling of spherical interpolyelectrolyte complexes

Mono-functionalized beta-cyclodextrins as simple and sensitive testbeds for implicit solvation methods and model systems of host-guest interactions

Specific Aspects of Counterion Condensation onto the Poly(styrene-sulfonate) Anion and Poly(allylammonium) Cation studied by Molecular Dynamics Simulations

IPEC Solver: inter-polyelectrolyte complex formation within Poisson-Boltzmann theory