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Unformatted text preview: Probing 2-D Reaction Coordinates of Amino Acid / Surface Binding BE 442 Research Proposal David Appleyard December 18, 2003 1 Abstract Binding interactions between oligo-molecules and surfaces have become important in many research fields. Specifically, these interactions can be extended to semiconductor self-assembly (1) for materials that are diﬃcult to produce industrially. A gradient force optical trap (op- tical tweezers) offers an intriguing method to investigate these interactions at a molecular level by allowing the extraction of a two dimensional reaction coordinate diagrams through elucidation of the force interactions between a probe molecule and a surface. These reaction coordinate diagrams can provide the strength and directionality of the interactions and can extend and expand research in the area of semiconductor self assembly as well as a broad range of other fields. 2 Motivation Gallium Nitride (GaN) has applications for solid state lighting, data storage, communication devices as well as many others. GaN can be used to make blue light emitting diodes, a much more energy eﬃcient lighting source(2). Unfortunately pure, defect-free, GaN is very diﬃcult to produce. However, new methods for crystal production using viruses for guided self-assembly are under investigation (1). Yet, the specific molecular interactions between the crystal structure and the self-assembly promoting amino acid chains provided by the virus are not well defined. The ability to precisely control, monitor, and manipulate the interactions between a surface and a protein is invaluable in quantifying the reaction coordinate and can lead to de- termination of molecular mechanisms and chemical transformations involved in the reaction. Current exploration in the areas of silicon-biology and biologically directed nano-fabrication would benefit from knowledge of these interactions. The recent developments in optical 1 2-D Reaction Coordinates for Surface Binding D. Appleyard tweezers and 2-D force clamping has opened the door to analytical measurement and deter- mination of these quantities. Possessing exact knowledge of the reaction coordinate of biological molecular reactions and the comprehension of the binding forces involved is instrumental in understanding the biological processes that are at the forefront of current research. This knowledge can be applied to GaN as well as a myriad of other semiconductors and other materials. 3 Background 3.1 Equipment and Technology Laser-based, gradient-force optical traps, also known as optical tweezers, allow the position- ing and control of objects whose characteristic dimensions are similar to the wavelength of light (3). These traps can place forces on the order of 200 pN with high, sub pN force res- olution on objects of interest and when combined with appropriate position sensing devices can detect sub-nanometer movement. This technology offers the ability to position or pull appropriately modified proteins on a controlled,...
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This note was uploaded on 11/11/2011 for the course BIO 2.797j taught by Professor Matthewlang during the Fall '06 term at MIT.
- Fall '06