people
|Faculty
|David Earl
 |
David Earl Department of Chemistry |
Research in the Earl group uses the tools of computer simulation
and statistical mechanics to study and explain chemical, biological, and material processes. A number of topics are currently of interest:
Coarse-Grained Models of Complex Molecular Species
The properties of mesomorphic materials composed of complex molecular species with novel architectures are of great interest. These include polyphilic, dendritic, block-copolymer, and rod-coil molecules. In these systems, microphase separation, induced by chemical interactions between different parts of molecules, can be used as a tool to build new materials that contain structures that are ordered on the nanoscale. The variety and complexity of the molecular species used are limited only by the imagination of the chemist. However, while the phase behavior of AB block copolymers may be relatively easy to predict, those of more complex molecular species are not and the prediction of phase behavior based only on the knowledge of chemical structure remains a key aim of computational chemistry. To reach this overall goal, we are developing coarse-graining procedures and new computer simulation techniques that can bridge both time and length scales.
Zeolite Nucleation and Hypothetical Structures
Zeolites are crystalline microporous materials that have a wide-range of applications. Zeolites are porous on the molecular scale with structures that contain regular arrays of channels that are on the order of 0.3 to 1.5 nm in size. These channels can be filled with water or other guest molecules and the molecular sieving ability of zeolites has led to the development of new types of selective separation processes (e.g. sorption and ion exchange) and in their acid form zeolites have many useful catalytic properties. Current research in this area is directed towards understanding the nucleation process during zeolite synthesis using computer simulation techniques. A better understanding of the nucleation event could lead to the discovery and synthesis of new materials with specific tailored properties, and the improvement of the performance of existing materials. We are also developing a database of hypothetical zeolite structures that might be thermodynamically accessible. We aim to mine this database for structures with useful material properties and, in conjunction with the nucleation project, suggest experimental conditions for the synthesis of these potentially new and useful materials.
Immune System Dynamics and Vaccine Design
Statistical mechanics is used to relate randomness and fluctuations at the microscopic level to macroscopic bulk properties. As correlations, diversity, randomness, and fluctuations play an important part in disease, pathogen evolution, and the immune system response to vaccination and disease exposure, methods from statistical mechanics can be important tools in the study of these systems. We are interested in the immune system response to pathogens that are troublesome due to their high evolutionary rates, such as influenza (including H5N1), HIV, and cancers, as well as autoimmune diseases. Fundamental questions that need to be answered in this field include how to design vaccines that are adept at evading the immune response and what the optimal treatment protocols to use are. In order to examine these important topics we use and develop models of protein structure and function, and utilize Monte Carlo simulations and genetic algorithms to mimic selection in the immune system and pathogen evolution.
Biological Evolution
Fundamental theories of biological evolution are of significant interest to the group. Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, because of the essentially infinite complexity of protein sequence space. Recent work has described how evolvability, or the capacity/propensity to evolve, can be an object of natural selection. Our research is focused on explaining how modularity, canalization, and robustness can evolve in biological systems and determining how these properties influence the evolution and evolvability of populations.
Awards
Junior Research Fellowship, Mansfield College, Oxford University (2005-2006).
Selected Publications
"Localization and Glassy Dynamics in the Immune System," J. Sun, D. J. Earl and M. W. Deem, Mod. Phys. Lett. B, 2006, 20, 63-95
"Parallel Tempering: Theory, Applications, and New Perspectives," D. J. Earl and M. W. Deem, Phys. Chem. Chem. Phys., 2005, 7, 3910-3916
"Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease," J. Sun, D. J. Earl and M. W. Deem, Phys. Rev. Lett., 2005, 95, 148104
"Induced and spontaneous deracemization in bent-core liquid crystal phases and in other phases doped with bent-core molecules," D. J. Earl, M. A. Osipov, H. Takezoe, Y. Takanishi and M. R. Wilson, Phys. Rev. E, 2005, 71, 021706
"Evolvability is a selectable trait," D. J. Earl and M. W. Deem, Proc. Natl. Acad. Sci. USA, 2004, 101, 11531-11536
"Optimal Allocation of Replicas to Processors in Parallel Tempering Simulations," D. J. Earl and M. W. Deem, J. Phys. Chem. B, 2004, 108, 6844-6849
"Calculations of helical twisting powers from intermolecular torques," D. J. Earl and M. R. Wilson, J. Chem. Phys., 2004, 120, 9679-9683
"Predictions of molecular chirality and helical twisting powers: A theoretical study," D. J. Earl and M. R. Wilson, J. Chem. Phys., 2003, 119, 10280-10288
"Computer simulations of soft repulsive spherocylinders," D. J. Earl, J. Ilnytskyi and M. R. Wilson, Mol. Phys., 2001, 99, 1719-1726