The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex s...

The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid comp...

The influence of electrostatic multipole moments up to hexadecapole on the dynamics of photodissociated carbon monoxide (CO) in myoglobin is investigated. The CO electrostatic potential is expressed as an expansion into atomic multipole moments of increasing order up to octopole which are obtained from a distributed multipole analysis. Three models with increasingly accurate molecular multipole...

Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electro...

An electrostatic model based on charge density is proposed as a model for future force fields. The model is composed of a nucleus and a single Slater-type contracted Gaussian multipole charge density on each atom. The Gaussian multipoles are fit to the electrostatic potential (ESP) calculated at the B3LYP/6-31G* and HF/aug-cc-pVTZ levels of theory and tested by comparing electrostatic dimer ene...

Post-translational modification by ubiquitin and ubiquitin-like (UBL) proteins is a key mechanism for cellular control. The specificity of the enzymes of ubiquitination and their close paralogs is dependent on their molecular electrostatic potentials. For example, analysis of molecular electrostatic potentials and electrostatically key residues can account for the selectivity of different E1s (...

Many signaling events require the binding of cytoplasmic proteins to cell membranes by recognition of specific charged lipids, such as phosphoinositol-phosphates. As a model for a protein-membrane binding site, we consider one charged phosphoinositol phosphate (PtdIns(3)P) embedded in a phosphatidylcholine bilayer. As the protein-membrane binding is driven by electrostatic interactions, continu...