Atomistic Approaches for the Analysis, Design, and Simulation of Nanosensors and Nanocatalysts

Abstract

Using ideas of materials genome initiative, it is possible to create new materials with tailored properties for applications in nanoelectronics, sensing, and catalysis among other fields. The contamination of groundwater due to accidental leakage of radioactive wastes poses a grave danger to the environment and human life and hence trace characterization of these radioactive materials is of paramount importance in nuclear forensics and reprocessing. The presence of uranium and plutonium complexes in contaminated soil and water around nuclear processing facilities especially after a nuclear accident would provide us with critical information to guide a proper and timely response. We examine the applicability of graphene-based nanosensor for detection of these radionuclides based on ab initio density functional theory and Green’s function theory. Changes in the molecular electrostatic potential due to presence of a foreign moiety near graphene can be transduced and amplified into current-voltage characteristics at nanoscale. By comparing the change in current due to presence of U or Pu complexes near a graphene-based sensor, we should be able to detect trace amounts of these radionuclides.

The DNA origami has emerged as a new and promising method to create nanostructures with precise atomistic tailored geometries. In addition, these origamis can be functionalized or impregnated with specialized single stranded DNA/RNA chains (known as aptamers) in order to convert them into biosensors. Thrombin is an enzyme directly involved in formation of blood clot which is a major cause of heart attack. We perform molecular dynamics simulations to determine the relative energetics associated with the capture of thrombin by a novel biosensor assembly consisting of two aptamers attached to a rectangular DNA origami.

In addition to developing nanosensors, we also apply multi-scale computational approach to develop nanocatalysts and describe catalytic reactions happening at the surface to design more efficient catalysts. Molybdenum disulfide, (MoS2) being a very versatile material for several applications, is an industrial catalyst for hydrotreating processes in petroleum refineries. We perform MD simulations on a typical middle distillate fraction of crude oil containing thiophene and dibenzothiophene molecules in order to determine their relative positions with respect to the catalytic surface previous to possible reactions that are then studied with DFT. Furthermore, we analyze MoS2- graphene and MoS2-boron nitride clusters as possible hydrodesulfurization catalysts.