Interaction of liquid water with the rutile TiO2 (110) surface

A force-field which describes the interaction between the TiO2 (110) rutile surface and a modified TIP3P water [P. Mark and L. Nilsson, J. Phys. Chem. A, 105, 9954, (200 1)] is tested against periodic density functional theory (PDFT). Optimizations of water on the non-hydroxylated and hydroxylated surfaces are performed using PDFT and the geometries are compared with optimizations of modified TIP3P water on the TiO2 surface using the force-field. The surface hydroxyl torsional profile is also compared using PDFT and force-field calculations as well as molecular dynamics (MD) simulations of the surface. MD simulations of liquid TIP3P water, containing dissolved Na+ and Cl- ions, on six TiO2 (110) surfaces at 298 K and 1 atm are performed for neutral surfaces and negatively-charged surfaces. Axial density and angular distributions show good agreement with results of Predota et al. [J. Phys. Chem. B, 108, 12049 (2004)] and X-ray crystal truncation rod experiments [Z. Zhang et al., Langmuir, 20, 4954 (2004)]

Side chain-positioning as an integer programming problem

Abstract. An important aspect of homology modeling and protein design algorithms is the correct positioning of protein side chains on a fixed backbone. Homology modeling methods are necessary to complement large scale structural genomics projects. Recently it has been shown that in automatic protein design it is of the uttermost importance to find the global solution to the side chain positioning problem [1]. If a suboptimal solution is found the difference in free energy between different sequences will be smaller than the error of the side chain positioning. Several different algorithms have been developed to solve this problem. The most successful methods use a discrete representation of the conformational space. Today, the best methods to solve this problem, are based on the dead end elimination theorem. Here we introduce an alternative method. The problem is formulated as a linear integer program. This programming problem can then be solved by efficient polynomial time methods, using linear programming relaxation. If the solution to the relaxed problem is integral it corresponds to the global minimum energy conformation (GMEC). In our experimental results, the solution to the relaxed problem has always been integral.

Parametric studies in multiscale modeling of high-performance polymers

A computational parametric study has been performed to establish the effect of Representative Volume Element (RVE) size, force field type, and simulation temperature on the predicted mechanical properties of polyimide and polycarbonate materials modeled atomisticially. The results of the simulations indicate no clear effect of RVE size and force field type on the predicted mechanical response of the polyimide and polycarbonate polymer systems. A multiscale modeling technique was utilized to determine the equivalentcontinuum Young\u27s moduli, density, and stress-strain behavior for the set of mentioned modeling parameters. Parametric studies also indicate no clear effect of the simulation temperature on the predicted material densities of LaRC-CP2 when the AMBER force field is used. However, the MM3 force field predicts a steady decrease in the density of LaRC-CP2 as the temperature increases up to and beyond the glass transition temperature. These force fields vary slightly in form and with the associated parameters