2017 Biomolecular Simulations, Nanopore Dynamics, Sliding Scales, Nanoscale Mechanisms

St. Edward’s University School of Natural Sciences is home to undergraduate majors spanning biology, bioinformatics, chemistry, math and computer science. Many exciting research endeavors spawn from intersections between these disciplines which was the theme of the 2017 Lucian Symposium: Computational Connections: Modeling Materials, Molecules & More. Each presentation highlighted unique research applications that incorporate knowledge from a number of disciplines to understand the complexity and potential applications of a variety of different systems described below:

teplowBiomolecular 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.

greigNanopore 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.

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?

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.

About the Brother Lucian Blersch Symposium

Organized by the School of Natural Sciences at St. Edward’s University, the event is free and open to the public. This symposium honors Brother Lucian Blersch, CSC, a longtime professor of Engineering at St. Edward’s who died in 1986 and in whose name a professorship in the School of Natural Sciences was endowed by a gift from J.B.N. Morris hs ’48, ’52, and his family.

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