Abstract:

1. Designing pattern recognition surfaces for selective adsorption of copolymer sequences : Most of the theoretical work in the area of the pattern recognition by biomimetic polymers has focussed on keeping the pattern on the heterogeneous surface fixed and allowing different types of copolymers to adsorb on the surface to determine the characteristics of the copolymer that can "recognize" the surface pattern. However, the question of how to design optimal surfaces or what pattern the surfaces should have for recognizing specific monomer sequences in copolymers, had not been answered yet. To address this issue, we have developed a novel simulation method to design surfaces for recognizing specific monomer sequences in copolymers. This work provides the foundation for future work in understanding many biological processes that rely on pattern recognition, such as transmembrane signaling, pathogen-host interactions, viral-inhibition, etc. (publication 1)

2. Pattern transfer in AB diblock copolymer film adsorbed on a heterogeneous surface: In this work we investigated how a pattern imposed in a copolymer film at a certain distance from the surface propagates through the film onto an adsorbing heterogeneous surface. We examined the effect of varying the copolymer chain length, the size of the target pattern, and the distance from the surface where the target pattern is applied, z', on the extent of pattern transfer. For each chain length, target pattern, and z' we compared the energy of the system when a pattern is applied in the bulk to the energy when no pattern is applied in order to understand why a certain pattern size is transferred to the surface with higher fidelity than the others. (publication 2)

3. Molecular recognition in model DNA microarrays : DNA microarrays has been widely adopted by the scientific community for a variety of applications to reconstruct the metabolic pathways for cell operation, to identify genes that are differentially expressed in healthy versus diseased cells, etc. In order to improve performance and to design next generation microarrays there is a need for a fundamental understanding of the interplay between the various factors that affect microarray performance. To gain such a fundamental understanding we study the thermodynamics and the kinetics of hybridization of single stranded "target" genes in solution with complimentary immobilized "probe" DNA molecules on a microarray surface using a coarse-grained lattice model. We use Monte Carlo simulations to examine how various parameters affect the extent of hybridization and the kinetics of the hybridization process. This work should give a fairly broad physical picture of molecular recognition in DNA microarrays and eventually provide a set of general guidelines for maximizing microarray sensitivity and specificity. (publications 4-6)