We report the design and development of a friction force microscope for high-resolution studies in electrochemical environments. The design choices are motivated by the experimental requirements of atomic-scale friction measurements in liquids. The noise of the system is analyzed based on a methodology for the quantification of all the noise sources. The quantitative contribution of each noise ...

We report here a test of the Semi-Explicit Assembly (SEA) model in the solvation free energy category of the SAMPL3 blind prediction event (summer 2011). We tested how dependent the SEA results are on the chosen force field by performing calculations with both the General Amber and OPLS force fields. We compared our SEA results with full molecular dynamics simulations in explicit solvent. Of th...

Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, an...

Successful ab initio folding of proteins with both -helix and -sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any / proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold / proteins with a force field emphasizing the balance between the two majo...

A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding s...