Employing recent advances in response theory and nonequilibrium ensemble reweighting, we study the dynamic static correlations that give rise to an electric field-dependent ionic conductivity electrolyte solutions. We consider solutions modeled with both implicit explicit solvents, different dielectric properties, at multiple concentrations. Implicit solvent models low concentrations small cons...

We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins...

The sequence fitness of a single-domain antibody with unusually high thermal stability is explored by a combined computational and experimental study. Starting with the crystallographic structure, RosettaBackrub simulations were applied to model sequence-structure tolerance profiles and identify key substitution sites. Experimental site-directed mutagenesis was used to produce a panel of mutant...

The SAMPL2 hydration free energy blind prediction challenge consisted of a data set of 41 molecules divided into three subsets: explanatory, obscure and investigatory, where experimental hydration free energies were given for the explanatory, withheld for the obscure, and not known for the investigatory molecules. We employed two solvation models for this challenge, a linear interaction energy ...

When attempting to compute thermodynamic quantities with a molecular simulation, we are frequently confronted with the problem of sampling in a high-dimensional configuration space. The dimensionality of this space is given by the number of degrees of freedom for the molecular system. Techniques which lower the number of degrees of freedom will increase the efficiency of the thermodynamic sampl...