? The goal of this project is to provide a molecular picture (theory) of DNA on surfaces in solution, which is consistent with known thermodynamic and structural data, which can be used to consider design optimization problems for a variety of experiments. A key question is understanding the experimentally observed changes in hybridization affinity and selectivity near surfaces for certain surface/solution condition combinations. ? Using theoretical methods, including analytic theory and molecular simulations, we will quantify the balance between general solution effects (such as screening and solvation) and specific effects due to the surface and molecular association in solutions in determining the thermodynamics of DNA. We will make detailed calculations with our new analytic methods and simulations in an attempt to make the most direct ? possible comparisons with recent and planned thermodynamic, structural and biophysical experiments. The relation of thermodynamic specificity, sensitivity of detection and the concentration of nucleotides to their solution/surface environment, including electric fields and salt concentration will be calculated. Test cases ? and applications have been chosen to maximize overlap with existing data or collaborations that will yield data of specific relevance to DNA analyses on surfaces. ? ?
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