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Novel methodology developments in mo...

Minary, Peter.

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Novel methodology developments in modern molecular simulations.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Novel methodology developments in modern molecular simulations./
作者:	Minary, Peter.
面頁冊數:	205 p.
附註:	Source: Dissertation Abstracts International, Volume: 65-12, Section: B, page: 6412.
Contained By:	Dissertation Abstracts International65-12B.
標題:	Chemistry, Physical. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3157839
ISBN:	9780496902811

Novel methodology developments in modern molecular simulations.
Minary, Peter.

Novel methodology developments in modern molecular simulations. - 205 p.

Source: Dissertation Abstracts International, Volume: 65-12, Section: B, page: 6412.

Thesis (Ph.D.)--New York University, 2005.

The present thesis aims to summarize novel methodological developments and their uses in the rapidly expanding field of molecular simulations. A new formalism designed to treat long range interactions on surfaces/wires, systems which are infinitely replicated in two/one spatial directions but have finite extent in the remaining dimensions, is developed in the first part of this thesis. The method is tested on both model and realistic problems and is found to be accurate, efficient and a marked improvement over existing formulations in speed, accuracy and utility. In the second part of this thesis, a novel ab initio molecular dynamics technique capable of treating metallic systems and highly exothermic chemical reactions is presented. The combination of the aforementioned methods are applied in the next part to study functionalization reactions at the Si(100)-2x1 semiconductor interface. Here, a set of forty finite temperature ab initio molecular dynamics trajectories is employed to investigate the microscopic mechanism of the addition of 1,3-butadiene to the Si(100)-2x1 surface. The detailed study of the trajectories indicate a common non-concerted stepwise mechanism that proceeds via an intermediate carbocation. In the remaining parts of the thesis, a novel set of methods is introduced to significantly enhance conformational sampling in molecular dynamics simulations of biomolecular systems. First, a new set of equations of motion and a reversible, resonance free, integrator are developed which permits step sizes on the order of 100 fs to be used. The new technique provides sufficient sampling to impact studies of the 200--300 residue proteins of greatest interest. Second, it is shown that combining molecular dynamics with novel variable transformations designed to warp configuration space so as to reduce barrier regions and enhance attractive basins lead to substantial gains in conformational sampling efficiency. Here, new transformations designed to overcome barriers induced by intermolecular interactions are introduced. The method is shown to substantially enhance conformational sampling in long alkane chains and in a model protein over standard molecular dynamics as well as parallel tempering.

ISBN: 9780496902811Subjects--Topical Terms:

560527
Chemistry, Physical.

Novel methodology developments in modern molecular simulations.
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