Biomolecular Simulations: Utilizing large scale compute resources and coupling together efficient and highly optimized AMBER molecular dynamics simulations on GPUs, we can rapidly converge the conformational ensembles of various nucleic acid motifs. This provides the means to assess and validate the molecular potentials or “force fields” and also to provide detailed insight into nucleic acid structure, dynamics, and function.

Nanopore Dynamics: Dramatic changes in the molecular-level structure and dynamics of liquids occur upon nanoscale confinement in mesoporous silica. Understanding the chemistry that occurs in these environments is still an outstanding challenge with implications for many important applications including catalysis, sensing, and energy generation. These issues will be discussed in the context of electronic structure calculations of the surfaces themselves and molecular dynamics simulations of liquids at interfaces with varying structure and surface functionalization. Comparisons to experimental results, where available, will be highlighted. A particular focus will be the molecular-level origins of the observed behavior, including those relevant to chemical processes, e.g., reactivity, solvation, molecular reorientation, and hydrogen-bond dynamics.

Nanoscale Mechanisms: As the renown physicist, Colin Humphreys, said, ‘Crystals are like people, it is the defects in them which tend to make them interesting!’ Recent research in the area of nanoscale materials modeling aims at uncovering the influence of defects and mechanisms (i.e., dislocations, twinning, and grain boundaries) on the strength, deformation, and stability of functional materials. Approaches that effectively merge high-performance computing and atomistic modeling have proven capable of providing unprecedented insight into key deformation processes underlying microstructure evolution in a myriad of materials. In particular, how these mechanisms compete leading to stronger materials using continuum mechanics theory will be presented in addition to a new mechanism in layered materials that could potentially lead to engineering materials with tunable properties.

Sliding Scales: Molecular modeling and computational chemistry is sometimes referred to as in silico chemistry, evoking notions of molecular ghosts trapped inside silicon computer chips.  But not every problem in predicting molecular structure requires a high-performance computer to solve. This presentation will explore the structures of highly strained and topologically intriguing molecules, including a series of [n] Möbiusenes. What can we learn from using paper and pencil that was not apparent from a B3YLP/6-31G(d) optimization?