Rattling modes and the intrinsic vibrational spectrum of beetle-type scanning tunneling microscopes

It is known that the vibrational spectra of beetle-type scanning tunneling microscopes with a total mass of ≈3–4 g contain extrinsic ‘rattling’ modes in the frequency range extending from 500 to 1700 Hz that interfere with image acquisition. These modes lie below the lowest calculated eigenfrequency of the beetle and it has been suggested that they arise from the inertial sliding of the beetle between surface asperities on the raceway. In this paper we describe some cross-coupling measurements that were performed on three home-built beetle-type STMs of two different designs. We provide evidence that suggests that for beetles with total masses of 12–15 g all the modes in the rattling range are intrinsic. This provides additional support for the notion that the vibrational properties of beetle-type scanning tunneling microscopes can be improved by increasing the contact pressure between the feet of the beetle and the raceway.

Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.