O(N) continuous electrostatics solvation energies calculation method for biomolecules simulations

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory requirements, is only a few percent wrong for any molecular configurations of arbitrary sizes, gives explicit value for the reaction field potential at any point, provides both the solvation energy and its derivatives suitable for Molecular Dynamics simulations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as solvation energies of molecular complex formation.Comment: 6 pages, 4 figures, more results, examples and references adde

A hybrid stabilization technique for simulating water wave - Structure interaction by incompressible Smoothed Particle Hydrodynamics (ISPH) method

The Smoothed Particle Hydrodynamics (SPH) method is emerging as a potential tool for studying water wave related problems, especially for violent free surface flow and large deformation problems. The incompressible SPH (ISPH) computations have been found not to be able to maintain the stability in certain situations and there exist some spurious oscillations in the pressure time history, which is similar to the weakly compressible SPH (WCSPH). One main cause of this problem is related to the non-uniform and clustered distribution of the moving particles. In order to improve the model performance, the paper proposed an efficient hybrid numerical technique aiming to correct the ill particle distributions. The correction approach is realized through the combination of particle shifting and pressure gradient improvement. The advantages of the proposed hybrid technique in improving ISPH calculations are demonstrated through several applications that include solitary wave impact on a slope or overtopping a seawall, and regular wave slamming on the subface of open-piled structure

Spectral Volume Method: application to Euler equations and performance appraisal

The compact high-order "Spectral Volume Method" designed for conservation laws on unstructured grids is presented. Its spectral reconstruction is exposed briefly and its applications to the Euler equations are presented through several test cases to assess its accuracy and stability. Comparisons with usual methods such as MUSCL show the superiority of SVM. The SVM method arises as a high-order accurate scheme, geometrically flexible and computationally efficient

An infrared spectroscopy study of the conformational evolution of the Bis(trifluoromethanesulfonyl)imide ion in the liquid and in the glass state

We measure the far-infrared spectrum of N,N-Dimethyl-N-ethyl-N-benzylammonium (DEBA) bis(trifluoromethanesulfonyl) imide (TFSI) ionic liquid (IL) in the temperature range between 160 and 307 K. Differential scanning calorimetry measurements indicate that such IL undergoes a glass transition around 210K. DFT calculations allow us to assign all the experimental absorptions to specific vibrations of the DEBA cation or of the two conformers of the TFSI anion. We find that the vibration frequencies calculated by means of the PBE0 functional are in better agreement with the experimental ones than those calculated at the B3LYP level, largely used for the attribution of vibration lines of ionic liquids. Experimentally we show that, in the liquid state, the relative concentrations of the two conformers of TFSI depend on temperature through the Boltzmann factor and the energy separation, ΔH, is found to be ≈2 kJ/mol, in agreement with previous calculations and literature. However, in the glassy state, the concentrations of the cis-TFSI and trans-TFSI remain fixed, witnessing the frozen state of this phase