Doctor of Philosophy / Department of Physics / Amit Chakrabarti / We carry out Brownian Dynamics Simulations to study the self-assembly of ligated gold nanoparticles for various ligand chain lengths. First, we develop a phenomenological model for an effective nanoparticle-nanoparticle pair potential by treating the ligands as flexible polymer chains. Besides van der Waals interactions, we incorporate both the free energy of mixing and elastic contributions from compression of the ligands in our effective pair potentials. The separation of the nanoparticles at the potential minimum compares well with experimental results of gold nanoparticle superlattice constants for various ligand lengths. Next, we use the calculated pair potentials as input to Brownian dynamics simulations for studying the formation of nanoparticle assembly in three dimensions. For dodecanethiol ligated nanoparticles in toluene, our model gives a relatively shallower well depth and the clusters formed after a temperature quench are compact in morphology. Simulation results for the kinetics of cluster growth in this case are compared with phase separations in binary mixtures. For decanethiol ligated nanoparticles, the model well depth is found to be deeper, and simulations show hybrid, fractal-like morphology for the clusters. Cluster morphology in this case shows a compact structure at short length scales and a fractal structure at large length scales. Growth kinetics for this deeper potential depth is compared with the diffusion-limited cluster-cluster aggregation (DLCA) model. We also did simulation studies of nanoparticle supercluster (NPSC) nucleation from a temperature quenched system. Induction periods are observed with times that yield a reasonable supercluster interfacial tension via classical nucleation theory (CNT). However, only the largest pre-nucleating clusters are dense and the cluster size can occasionally range greater than the critical size in the pre-nucleation regime until a cluster with low enough energy occurs, then nucleation ensues. Late in the nucleation process the clusters display a crystalline structure that is a random mix of fcc and hcp lattices and indistinguishable from a randomized icosahedra structure. Next, we present results from detailed three-dimensional Brownian dynamics simulations of the self-assembly process in quenched short-range attractive colloids. Clusters obtained in the simulations range from dense faceted crystals to fractal aggregates which show ramified morphology on large length scales but close-packed crystalline morphology on short length scales. For low volume fractions of the colloids, the morphology and crystal structure of a nucleating cluster are studied at various times after the quench. As the volume fraction of the colloids is increased, growth of clusters is controlled by cluster diffusion and cluster-cluster interactions. For shallower quenches and low volume fractions, clusters are compact and the growth-law exponent agrees well with Binder–Stauffer predictions and with recent experimental results. As the volume fraction is increased, clusters do not completely coalesce when they meet each other and the kinetics crosses over to diffusion-limited cluster-cluster aggregation (DLCA) limit. For deeper quenches, clusters are fractals even at low volume fractions and the growth kinetics asymptotically reaches the irreversible DLCA case.

Master of Science / Department of Physics / Robert Szoszkiewicz / Proteins are involved in many of the essential cellular processes, such as cell adhesion, muscle function, enzymatic activity or signaling. It has been observed that the biological function of many proteins is critically connected to their folded conformation. Thus, the studies of the process of protein folding have become one of the central questions at the intersection of biophysics and biochemistry. We propose to use the changes of the nanomechanical properties of these biomolecules as a proxy to study how the single proteins fold. In the first steps towards this goal, the work presented in this thesis is concentrated on studies of unfolding forces and pathways of one particular multidomain protein, as well as on development of the novel method to study elastic spring constant and mechanical energy dissipation factors of simple proteins and peptides. In the first part of this thesis we present the results of the mean unfolding forces of the NRR region of the Notch1 protein. Those results are obtained using force spectroscopy techniques with the atomic force microscope (AFM) on a single molecule level. We study force-induced protein unfolding patterns and relate those to the conformational transitions within the protein using available crystal structure of the Notch protein and molecular dynamics simulations. Notch is an important protein, involved in triggering leukemia and breast cancers in metazoans, i.e., animals and humans. In the second part of this thesis we develop a model to obtain quantitative measurements of the molecular stiffness and mechanical energy dissipation factors for selected simple proteins and polypeptides from the AFM force spectroscopy measurements. We have developed this model by measuring the shifts of several thermally excited resonance frequencies of atomic force microscopy cantilevers in contact with the biomolecules. Next, we provided partial experimental validation of this model using peptide films. Ultimately, our results are expected to contribute in the future to the developments of medical sciences, which are advancing at a level, where human health and disease can be traced down to molecular scale.

Doctor of Philosophy / Department of Physics / Bruce M. Law / Three diverse first author surfaces science experiments conducted by Sean P. McBride 1-3 will be discussed in detail and supplemented by secondary co-author projects by Sean P. McBride, 4-7 all of which rely heavily on the use of an atomic force microscope (AFM). First, the slip length parameter, b of liquids is investigated using colloidal probe AFM. The slip length describes how easily a fluid flows over an interface. The slip length, with its exact origin unknown and dependencies not overwhelming decided upon by the scientific community, remains a controversial topic. Colloidal probe AFM uses a spherical probe attached to a standard AFM imaging tip driven through a liquid. With the force on this colloidal AFM probe known, and using the simplest homologous series of test liquids, many of the suspected causes and dependencies of the slip length demonstrated in the literature can be suppressed or eliminated. This leaves the measurable trends in the slip length attributed only to the systematically varying physical properties of the different liquids. When conducting these experiments, it was realized that the spring constant, k, of the system depends upon the cantilever geometry of the experiment and therefore should be measured in-situ. This means that the k calibration needs to be performed in the same viscous liquid in which the slip experiments are performed. Current in-situ calibrations in viscous fluids are very limited, thus a new in-situ k calibration method was developed for use in viscous fluids. This new method is based upon the residuals, namely, the difference between experimental force-distance data and Vinogradova slip theory. Next, the AFM’s ability to acquire accurate sub nanometer height profiles of structures on interfaces was used to develop a novel experimental technique to measure the line tension parameter, τ, of isolated nanoparticles at the three phase interface in a solid-liquid-vapor system. The τ parameter is a result of excess energy caused by the imbalance of the complex intermolecular forces experienced at the three phase contact line. Many differences in the sign and magnitude of the τ parameter exist in the current literature, resulting in τ being a controversial topic.