Simulation of biopolymer conformations

A necessary component of any real-life simulation of biopolymer conformations is the account of water. Water properties change with temperature and result in the temperature dependence of polymer-water interactions. On the other hand, polymer conformation changes itself with temperature. In a sum this shows up, for example, in well-known temperature dependence of hydrophobic effect. Thus arises a need to adjust the potentials that describe the interactions inside a biopolymer for this temperature-dependence due to water. Explicit account of water is difficult and computationally very expensive, on the other hand, analitycal theory allows to sum out solvent degrees of freedom and to derive the temperature-dependent transformation formula for the potentials, thus providing a way to describe the water-polymer interaction in implicit and computationally inexpensive way. We have solved such a problem by deriving the exact form of such transformation and are now interested in checking its validity and applicability on the example problems. We are looking for a collaboration with an experimental lab that is doing a qualitative comparison of their measured results against simulations. What we offer is the adjustment of the software they use and to include the effects of water. For example, it could be an RD department of pharmaceutical company, facing problems in finding agreement between measured and computed results at pre-production stage.