Shirts, Michael R.
The development of computational tools that can fundamentally change molecular design; drug design through prediction of physical properties and binding affinities and the design of novel biomimetic materials.
Computer simulations of molecular phenomena are increasingly successful aids to chemical engineering , bioengineering , and materials science. In most cases , experiments will be superior to simulations for answering molecular questions. However , simulation is particularly suited for (1) providing all-atom insight that is inaccessible through experiment and for (2) investigating large numbers of chemical entities and conditions that are expensive or difficult to physically create. As computer power continues to increase exponentially , atomistic simulation will become an even more important tool in the scientific and engineering arsenal.
Some of the specific problems that my research group will focus on are:
Overcoming drug resistance using quantitative ligand binding simulations.
One of the biggest challenges in antiviral drug design is overcoming acquired drug resistance. Most traditional informatics based methods are insufficiently sensitive to identify molecular variants that can effectively act against diverse viral mutants. However , atomistic simulations are approaching the point where they can be used to as an effective tool for rapidly prototyping useful new drugs.
Designing nonnatural heteropolymers for biological and materials applications.
The wide physical and chemical diversity of biological processes, achieved with a very limited set of chemical building blocks, suggests that the possibilities for introducing novel function in human-engineered materials are far beyond our current capabilities. Designed materials can draw from a much larger range of chemical structure and functionality than exists biologically. If we can add significant chemical diversity to Nature's already impressive toolkit, what else can be created?
Developing novel simulation algorithms for improved simulations.
Physics based simulations at the molecular level are extremely computationally intensive. For condensed phase materials , it is often very difficult to observe the timescales of many molecular phenomena of interest. As we begin to functionalize materials at the nanoscale , there is a great need for improved algorithms and methods to study molecular systems, using improved hardware, software, and theory.