Helix-coil transitions in polyalanine molecules of length 10 are studied by multi-canonical Monte Carlo simulations. The solvation effects are included by either a distance-dependent dielectric permittivity or by a term that is proportional to the solvent-accessible surface area of the peptide. We found a strong dependence of the characteristics of the helix-coil transition from the details of ...

Accurate ship detection from radar imagery needs a proper statistical characterization of both target and sea scattering. Even if a statistical model for the target class is not available, effective discrimination between “sea” and “nonsea” classes can be achieved making use of a good model for the sea scattering distribution (i.e. anomaly detection). Hence, the retrieval of the statistical cha...

We review recent developments of fast analytical methods for macroscopic electrostatic calculations in biological applications, including the Poisson-Boltzmann (PB) and the generalized Born models for electrostatic solvation energy. The focus is on analytical approaches for hybrid solvation models, especially the image charge method for a spherical cavity, and also the generalized Born theory a...

In this work, 242 NMR spin–spin coupling constants (SSCC) in 20 molecules are calculated, either with correlated wave function methods, SOPPA and HRPA(D), or density functional theory based on the B3LYP, BHandH, PBE0 functionals. The calculations were carried out without treatment of solvation via a polarizable continuum model both geometry optimization step and/or SSCC calculation, thereby, fo...

We implement a well-established concept to consider dispersion effects within a PoissonBoltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters are determined by comparison to experimental data as well as high level Quantum Mechanical reference calculations. The method is general and can be easily exten...

The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential combining a hard core repulsion and a longer ranged soft core interaction, yet exhibits water-like anomalies. The results are compared with equivalent calculatio...

Retention times in reversed-phase liquid chromatography were quantitatively analyzed in silico using alkanes as standard compounds, much like they have been used for Kovats indices in gas chromatography. The molecular interaction energy was calculated between an analyte and a model hydrophobic phase using a molecular mechanics program. The solvation energy was calculated between an analyte and ...

Atomic surface tensions are parameterized for use with solvation models in which the electrostatic part of the calculation is based on the conductor-like screening model (COSMO) and the semiempirical molecular orbital methods AM1, PM3, and MNDO/d. The convergence of the calculated polarization free energies with respect to the numerical parameters of the electrostatic calculations is first exam...