Xu, Muyi Ant (2014) Molecular dynamics approach to mica surface reconstruction. Masters thesis, Memorial University of Newfoundland.
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Mica has a layered silicate sheet structure and is widely used as a substrate for imaging biological samples. Due to its high thermal stability and negatively charged features, it is interesting to investigate whether the mica substrate will affect sample surface structure by enabling interactions between biological systems. In particular one has to consider the interactions of fluid or environmental water as well as associated ions with mica itself. Experimentally, previous research group members have observed protein alignment on the mica surface in register with underlying crystal directions. In particular, it is not clear how the protein and mica structures are connected across several length scales. We apply molecular dynamics (MD) calculations to investigate whether the mica substrate affects ordering of the ions in water. We first optimize the mica structure with four K⁺ ions originally in the system. Then we use two methods to check whether ions effect the mica surface reconstruction. The two methods are: replacing K⁺ ions with Na⁺ ions and removing ions from the mica system. Our calculations show that K⁺ and Na⁺ ions induce different surface reconstruction of mica. Furthermore, ion arrangements on the mica surface play an important role in water pattern formation. In this way, the nanoscale crystallographic reconstruction of the mica surface may be translated into a micro-scale pattern for protein alignment.
|Item Type:||Thesis (Masters)|
|Additional Information:||Includes bibliographical references (pages 70-78).|
|Department(s):||Science, Faculty of > Computational Science|
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