A (general) preferential entailment is defined by a “preference relation” among “states”. States can be either interpretations or sets of interpretations, or “copies” of interpretations or of sets of interpretations, although it is known that the second kind and the fourth one produce the same notion. Circumscription is a special case of the simplest kind, where the states are interpretations. ...

Kosmotropic (order-making) and chaotropic (order-breaking) co-solvents influence stability and biochemical equilibrium in aqueous solutions of proteins, acting indirectly through the structure and dynamics of the hydration water that surrounds the protein molecules. We have investigated the influence of kosmotropic and chaotropic co-solvents on the hydrogen bonding network dynamics of both bulk...

The effects of cosolvents on the solubility and hydration of small nonpolar solutes in solution has been investigated using a combination of molecular dynamics simulation and Widom particle insertion calculations. Results were obtained for helium, neon, argon, and methane solutes in solutions of sodium chloride, ammonium sulfate, calcium chloride, ammonium acetate, tetramethylammonium chloride,...

Nature has selected osmolytes to protect intracellular macromolecules against denaturing stress conditions. These molecules are accumulated in the intracellular environment at considerably high concentrations. In general, osmolytes are known to stabilize proteins. However, under certain conditions, their destabilizing properties have also been pointed out. A careful qualitative and quantitative...

The mechanism of denaturation of proteins by urea is explored by using all-atom microseconds molecular dynamics simulations of hen lysozyme generated on BlueGene/L. Accumulation of urea around lysozyme shows that water molecules are expelled from the first hydration shell of the protein. We observe a 2-stage penetration of the protein, with urea penetrating the hydrophobic core before water, fo...

It is well-known that the typical protein’s three-dimensional structure is relatively unstable in harsh conditions. A practical approach to maintain the folded state and thus improve the stability and activity of proteins in unusual circumstances is to directly apply stabilizing substances such as osmolytes to the protein-containing solutions. Osmolytes as natural occurring organic molecules ty...