AFM Investigation of Biological Nanostructures

Abstract

Nanostructures created by living organisms, optimized through millions of years of evolution, can be a valuable inspiration for nanotechnology. We employ atomic force microscopy to examine such structures in materials created by common organisms caddisy and diatoms. Caddisy larvae are well known for their ability to spin silk, which serves as an adhesive tape to glue various materials and collect food in aqueous environment. Atomic force microscopy imaging of caddisy silk, performed for the rst time by our team, has shown that its surface is patterned with 150 nm extensions a feature related to its exceptional underwater sticking abilities. Results of force spectroscopy of protein structures found on the surface are also shown. A characteristic feature of diatoms is that they are encased within a unique silica cell wall called frustules, patterned with 200 nm pores, which allow cellular interaction with the environment. We perform atomic force microscopy imaging of frustules in living diatoms as well as adhesion measurements inside pores.

Dancing on Water: The Choreography of Sulfur Dioxide Adsorption to Aqueous Surfaces

“…SMD was then performed on the 50 system configurations (in both the neat-water and saturated configurations) to guide the SO 2 down toward a tethered water near the water slab’s center of mass by applying a small steering force to the SO 2 -sulfur atom. This steering technique has been previously developed and used to successfully model chemical events. − The SO 2 thus passed through the continuum of environments from gas phase to (neat- and saturated) water surface adsorption, and finally absorption into the bulk of the H 2 O slab. Each of the SMD simulations were performed for a total of 200 ps, using a time step of 1 fs, and taking snapshots of the system every 25 fs.…”

Exploring the free-energy landscapes of biological systems with steered molecular dynamics

“…10, a non-equilibrium PMF type of approach has been developed on the basis of the Brownian dynamics fluctuation-dissipation theorem (BD-FDT), 11 extracting the equilibrium free-energy differences from the non-equilibrium, irreversible work measurements in steered molecular dynamics (SMD) simulations. [12][13][14][15][16][17][18][19] The precision and efficiency of the BD-FDT approach have been demonstrated with the coil-helix transition of the deca-alanine peptide. Preliminary results have been obtained for water 10 and glycerol transport 20 through aquaglyceroporin GlpF.…”