Analzying questioned documents in a nondestructive nature has been an issue for the forensic science community. Using nondestructive techniques such as video spectral comparator does not give reliable information due to the variations in gray or color levels that are distinguished differently by analysts. Destructive techniques such as chromatography give dependable, qualitative and quantitative, information but involves altering the evidentiary value of these questioned documents. The paradox of document examination becomes a problem when document evidence is involved, especially when trying to preserve its evidentiary value and critical data is needed. Thus, a nondestructive technique has been developed to solve the loopholes in document examinations. Direct analyte-probed nanoextraction (DAPNe) is a nanomanipulation technique that extracts ink directly off the document for further examination. A watermark is left, at most, post-extraction. DAPNe utilizes a tip emitter, pre-filled with a solvent, which is controlled in x-, y-, and z-coordinates via joystick controller and aspirates/extracts using a pressure injector. The versatility of this technique lies within the solvent chemistry and its capability to be coupled to various types of instrumentation. The extraction solvent can be altered to target specific components in the ink. For example, a chelator may be added to target metal …

This dissertation details the use of computational methods to understand the effect that cancer-related mutations have on proteins that complex with nucleic acids. Firstly, we perform molecular dynamics (MD) simulations of various mutations in DNA polymerase κ (pol κ). Through an experimental collaboration, we classify the mutations as more or less active than the wild type complex, depending upon the incoming nucleotide triphosphate. From these classifications we use quantum mechanics/molecular mechanics (QM/MM) to explore the reaction mechanism. Preliminary analysis points to a novel method for nucleotide addition in pol κ. Secondly, we study the ten-eleven translocation 2 (TET2) enzyme in various contexts. We find that the identities of both the substrate and complementary strands (or lack thereof) are crucial for maintaining the complex structure. Separately, we find that point mutations within the protein can affect structural features throughout the complex, only at distal sites, or only within the active site. The mutation's position within the complex alone is not indicative of its impact. Thirdly, we share a new method that combines direct coupling analysis and MD to predict potential rescue mutations using poly(ADP-ribose) polymerase 1 as a model enzyme. Fourthly, we perform MD simulations of mutations in the protection of …