Several simulation methods are currently in use to study peptide and protein folding. They can be classified in three groups depending on how the solvent is treated. At the simplest level, the solvent is ignored. At a second level, solvent effects are implicitly represented in the atomic interaction function. At the third level, solvent degrees of freedom are treated explicitly. We have perform...

A unique coarse-grained modeling scheme that combines a systematic, solvent-free multiscale coarse-graining algorithm for a complex macromolecule with an existing coarse-grained solvent model is proposed. We show that this procedure efficiently and reliably describes the interactions for complex macromolecules, using the specific example of dendrimers binding phenanthrenes in water. The experim...

The solvent-assisted lipid bilayer (SALB) method offers a general strategy to fabricate supported lipid bilayers on solid surfaces. In this method, lipids dissolved in alcohol are deposited on the target substrate in parallel with their aggregation during exchange with aqueous buffer solution which promotes spontaneous bilayer formation. Herein, a combination of experimental and theoretical app...

Integral equation theory is used for extrapolating free energy data from molecular simulations of a reference state with respect to a modification of the interaction potential. The methodology is applied to the correction of artefacts arising from potential shifting and truncation. Corrective contributions for the hydration free energy with respect to the full potential are analysed for the cas...

By molecular dynamics simulation of a coarse-grained bead-spring-type model for a cylindrical molecular brush with a backbone chain of N(b) effective monomers to which with grafting density σ side chains with N effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range 5 ≤ N ≤ 40, backbone chain lengths are...

The heat capacity has played a major role in relating microscopic and macroscopic properties of proteins and their disorder-order phase transition of folding. Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures, their solvent environment, and configurational averaging. To better understand these factors on c...