Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation

Recently advances in biological science have been dependent in corresponding advances in the field of DNA and protein separation. It therefore also requires the progress of the related electro-mechanical devices, in terms accuracy and speed of analysis. Most of these devices are composed of micro- a...

Full description

Saved in:
Bibliographic Details
Main Author: Emadaldin Moeendarbary
Other Authors: Lam Khin Yong
Format: Theses and Dissertations
Language:English
Published: 2010
Subjects:
Online Access:https://hdl.handle.net/10356/42231
Tags: Add Tag
No Tags, Be the first to tag this record!
Institution: Nanyang Technological University
Language: English
id sg-ntu-dr.10356-42231
record_format dspace
spelling sg-ntu-dr.10356-422312023-03-11T17:48:50Z Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation Emadaldin Moeendarbary Lam Khin Yong Ng Teng Yong School of Mechanical and Aerospace Engineering DRNTU::Engineering::Bioengineering Recently advances in biological science have been dependent in corresponding advances in the field of DNA and protein separation. It therefore also requires the progress of the related electro-mechanical devices, in terms accuracy and speed of analysis. Most of these devices are composed of micro- and/or nano- channels which involve flow of complex phenomena. Our focus is on these micro/nano channel devices, consisting of many entropic traps, which were designed and fabricated for the separation of long DNA molecules. The channel comprises narrow constriction and wider regions that cause sizedependent trapping of DNA at the onset of a constriction. This process creates electrophoretic mobility differences, thus enabling efficient separation without gel matrix or pulsed electric fields [1-3]. Simulation and in particular numerical simulation is an efficient way to investigate the complex flow in the related electro-mechanical devices. Investigations for different simulation methods were carried out and we came into conclusion that the Dissipative Particle Dynamics method, which groups a number of atoms/molecules into particles, is most suitable for the above-mentioned applications. MASTER OF ENGINEERING (MAE) 2010-10-04T05:54:33Z 2010-10-04T05:54:33Z 2009 2009 Thesis Emadaldin Moeendarbary. (2009). Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation. Master’s thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/42231 10.32657/10356/42231 en 164 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Engineering::Bioengineering
spellingShingle DRNTU::Engineering::Bioengineering
Emadaldin Moeendarbary
Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
description Recently advances in biological science have been dependent in corresponding advances in the field of DNA and protein separation. It therefore also requires the progress of the related electro-mechanical devices, in terms accuracy and speed of analysis. Most of these devices are composed of micro- and/or nano- channels which involve flow of complex phenomena. Our focus is on these micro/nano channel devices, consisting of many entropic traps, which were designed and fabricated for the separation of long DNA molecules. The channel comprises narrow constriction and wider regions that cause sizedependent trapping of DNA at the onset of a constriction. This process creates electrophoretic mobility differences, thus enabling efficient separation without gel matrix or pulsed electric fields [1-3]. Simulation and in particular numerical simulation is an efficient way to investigate the complex flow in the related electro-mechanical devices. Investigations for different simulation methods were carried out and we came into conclusion that the Dissipative Particle Dynamics method, which groups a number of atoms/molecules into particles, is most suitable for the above-mentioned applications.
author2 Lam Khin Yong
author_facet Lam Khin Yong
Emadaldin Moeendarbary
format Theses and Dissertations
author Emadaldin Moeendarbary
author_sort Emadaldin Moeendarbary
title Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
title_short Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
title_full Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
title_fullStr Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
title_full_unstemmed Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
title_sort dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation
publishDate 2010
url https://hdl.handle.net/10356/42231
_version_ 1761781341211328512