Julia Baldauf

Nanosensors for next generation drug screening

One promising path for future drug screening technologies is to examine the binding of ligands to target proteins at the single molecule level by passing them through nanometer sized pores and measuring the change in pore current during translocation. With the aim of evaluating such technologies we perform virtual experiments on the translocation of proteins through silicon nitride nanopores. These simulations consist of large scale, fully atomistic models of the translocation process that involve steering a test protein through the nanopore on a timescale of tens of nanoseconds. We make a comparison between theoretically expected and simulated values of the current drop that is seen when the protein occupies the pore. Details of the stability of the protein and the preservation of its function as measured by its secondary and tertiary structure will be presented to validate both the simulation results and the fundamental design of the proposed device. Finally, the results will be placed in the context of experimental work that combines nanofabrication and microuidics to create a high throughput, low cost, drug screening device.

Size-Dependent Fullerene–Fullerene Interactions in Water: A Molecular Dynamics Study

Nested fullerenes display a range of unique properties influenced by their size and shape. In this paper, the size- and shape-dependent aggregation of nested fullerenes in water is studied using explicit solvent molecular dynamic simulations. It is shown that water forms a layered structure near the surface of the particle, with the density of interfacial water increasing with increasing particle size. Meanwhile, water molecules near the extended facets of large nested fullerenes are unable to maintain their hydrogen bonding network, leading to a shape and size mediated structuring of surrounding waters. These distortions affect the overall association kinetics of particles in water with spherically shaped particles transitioning quickly into contact, while larger fullerenes, characterized by a lower sphericity, cluster at a much slower rate.

Simulations of graphitic nanoparticles at air–water interfaces

The free energy associated with transferring a set of fullerene particles through a finite water layer is calculated using explicit solvent molecular dynamic simulations. Each fullerene particle is a carbon network of one or more spheroidal shells of graphitic carbon, and include single-shell (single-wall) or nested multi-shelled (nano-onions) structures ranging from 6 to 28 Å in radius. Corresponding changes in energy suggest a stronger affinity of carbon nano-onions for water compared to their single-shelled analogues. In the case of multi-shelled structures, the free energy profiles display a global minimum only in the bulk liquid indicating a high affinity of multi-shelled fullerene for complete hydration. Single-wall particles however, display a minimum at the air-water interface and for particles larger than 2 nm this minimum is a global minimum possessing a lower energy compared to the particles state of complete hydration. While the propensity for single-shell particles to adsorb to the air-interface may increase with increasing particle size, there is an indication based on line tension calculations that larger single-shell particles may actually exhibit enhanced wetting compared to their smaller analogues.