Browsing by Author "Nunes, Nicole Lynne"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    A flexible lattice model to study protein folding
    (1996) Nunes, Nicole Lynne; Hutchinson, John S.
    The biological activity of protein molecules is central to life. It has been known for decades that this biological activity is dependent on the protein molecule achieving a particular geometric conformation. Simple lattice models have been developed to investigate the protein folding pathway since all-atom molecular dynamics simulations on the time scale of folding are beyond the current capabilities of computers. We present a new Monte Carlo lattice model to study the folding of heteropolymer chains. Previous lattice model studies of two-dimensional chains have been performed on square grids using pre-defined "move sets" of allowed moves. The motion of the polymer chain in these models is thus highly constrained. In order to add greater flexibility, we use a triangular lattice and allow the chain to choose its own moves. Physically unrealistic moves are prevented by including kinetic energy effects in the Metropolis algorithm. By looking at the results, we are able to characterize all of the possible one and two particle moves in the two-dimensional model and sort them according to relative importance. This information will be used to guide simplified molecular dynamics studies. We also find that the initial phase of the folding process is a rapid collapse to a relatively compact state which is entropically driven. The model has been extended to three dimensions. The increased difficulty of working in three-dimensions as well as the preliminary results will be discussed.
  • Thumbnail Image
    Item
    Ultra high vacuum scanning tunneling microscopy to study thin film growth
    (1994) Nunes, Nicole Lynne; Rau, Carl
    An ultra high vacuum chamber was constructed to study thin film growth using scanning tunneling microscopy (STM). The sample stage is specially designed so that samples can be transferred in situ among various film preparation techniques. For first studies, Ru thin films were deposited at sub-monolayer coverages on C(0001) substrates. From our STM studies, it is found that Ru diffuses easily along the graphite surface, that Ru atoms tend to nucleate at defect sites, and that the first monolayer of Ru grows homogeneously on graphite. These results are in agreement with our recent Auger electron spectroscopy data.