The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β-secretase binding complexes. This ...

The charge density of vector particles, for example W(+/-), may change sign. The effect manifests itself even for a free propagation, when the energy of the W-boson satisfies epsilon>sqrt[2]m and the standing wave is considered. The charge density of W also changes sign in a vicinity of a Coulomb center. For an arbitrary vector boson (e.g., for spin 1 mesons), this effect depends on the g-facto...

In this Brief Report, we perform molecular-dynamics simulations of an interface containing charged functional groups of different valences in contact with 2:1 ionic solution. We take into account both the finite sizes of the ions in solution and the functional groups but we neglect the structural details of the solvent (primitive model). We show that the interaction between a charged interface ...

The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions...

We analyze bulk diffusion and transport through hydrophobic nanochannels of nanoparticles (NPs) with different hydrophobic-hydrophilic patterns achieved by coating a fraction of the NP sites with positive or negative charges via explicit solvent molecular dynamics simulations. Ten different charge pattern types including Janus charged-hydrophobic NPs are studied. The cationic NPs are more affec...

interaction and correlation effects in quantum dots play a fundamental role in defining both their equilibrium and transport properties. numerical methods are commonly employed to study such systems. in this paper we investigate the numerical calculation of quantum transport of electrons in spherical centered defect ingaas/algaas quantum dot (scdqd). the simulation is based on the imaginary time...

Hemicelluloses can be removed from wood chips prior to mechanical pulping, which would offer new feedstocks for the production of chemicals and fuels. The aim of this study was to evaluate pre-extraction to maximize pre-extraction yield, while minimizing negative impacts on wood chips. The effects of three independent process variables (NaOH charge, pre-extraction temperature, and time) on thre...

soil colloid particles influence soil chemical and physical properties by their surface electrical charge. with respect to the importance of this issue from both agricultural and environmental points of view, charging behavior of a kaolinite sample was studied in the ph range of 4 to 10 and at three background electrolyte concentrations, including 0.005, 0.05, 0.5 m nacl, by potentiometric titr...

In this lecture we present some interesting issues that arise when the dynamics of the charge carriers in the CuO2 planes of the high temperature superconductors is considered. Based on the qualitative picture of doping, set by experiments and some previous calculations, we consider the strength of various inter and intra-cell charge transfer susceptibilities, the question of Coulomb screening ...

Photoinduced charge separation in a mixture of Perylene Red (N,N'-bis(2,6-di-isopropylphenyl)-1,6,7,12-tetraphenoxyperylene-3,4:9,10-tetracarboxylic acid bis-imide) and pyrene, organized in thin solid film on quartz, was studied by means of steady-state absorption and emission spectroscopy and by femtosecond transient absorption spectroscopy. Steady state spectroscopy shows substantial interact...