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 ) 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 electrostatic determinants 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-Hu ckel 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