Published in Journal of computer-aided molecular design
The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of integral equation formalism. Several force field parameters have been tested...
Published in Journal of Sol-Gel Science and Technology
AbstractInorganic–organic hybrid polymers are promising alternatives to simple organic polymers. They combine the advantages of organic and inorganic components in one homogeneous material, which can be adjusted to match sophisticated demands for various possible applications ranging from soft silicones to hard hybrid ceramics. Typically, the inorg...
Published in Comprehensive Biophysics
Molecular dynamics (MD) simulation is becoming an invaluable tool for studying biomolecular structure and dynamics, the relationship between which is central to understanding important cellular processes. This chapter surveys recent technological developments that have enabled all-atom MD simulation on timescales orders of magnitude longer than was...
Published in European Biophysics Journal
We have studied two different β-peptides in methanol using explicit solvent molecular dynamics simulations and the GROMOS 53A6 force field: a heptapeptide (peptide 1) expected to form a left-handed 314-helix, and a hexapeptide (peptide 2) expected to form a β-hairpin in solution. Our analysis has focused on identifying and analyzing the stability o...
