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An embedded cluster model is used to estimate the molecular dipole moment of crystalline dimethylnitramine (DMNA). The electrostatic potential due to the crystal is included in the calculation via the SCREEP (surface charge representation of the electrostatic embedding potential) approach. The resulting dipole moment for DMNA in the crystalline environment is 6.69 D. This number is more than 40...

Classical molecular dynamics simulations with polarizable potential models were carried out to quantitatively determine the effects of KCl salt concentrations on the electrostatic surface potentials of the vapor-liquid interface of water. To the best of our knowledge, the present work is the first calculation of the aqueous electrolyte surface potentials. Results showed that increased salt conc...

Reliable determination of the surface potential with spatial resolution is key for understanding complex interfaces that range from nanostructured surfaces to molecular systems to biological membranes. In this context, Kelvin probe force microscopy (KPFM) has become the atomic force microscope (AFM) method of choice for mapping the local electrostatic surface potential as it changes laterally d...

electrostatic potential as well as the local volume charge density are computed for a macromolecule by solving the poisson-boltzmann equation (pbe) using the finite element method (fem). as a verification, our numerical results for a one dimensional pbe, which corresponds to an infinite-length macromolecule, are compared with the existing analytical solution and good agreement is found. as a ma...

The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shap...

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...

This paper introduces a self-consistent computational protocol for modeling protein electrostatic potentials according to static point-charge model distributions. The protocol involves a simple space-domain decomposition scheme where individual molecular domains are modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) protein environment. Electr...

BACKGROUND A total of 12 phenylpropanoid amides were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity, tumor selectivity and anti-HIV activity, in order to investigate on their biological activities. MATERIALS AND METHODS Cytotoxicity against four human oral squamous cell carcinoma (OSCC) cell lines and three human oral normal cells was de...