Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

Nanotechnology

Volumn 18, Issue 13, 2007, Pages

  Wang, Guan M ^a   Sandberg, William C ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MOLECULES; MOLECULAR DYNAMICS SIMULATIONS; MULTISCALE SIMULATIONS; RESPONSE DYNAMICS;

CHANNEL FLOW; COMPUTER SIMULATION; MOLECULAR DYNAMICS; NANOSTRUCTURED MATERIALS; QUANTUM THEORY; SHEAR FLOW;

DNA;

6 MERCAPTO 1 HEXANOL; DNA; DOUBLE STRANDED DNA; GOLD; HEXANOL; NANOCHANNEL; SINGLE STRANDED DNA; SOLVENT; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; DENSITY FUNCTIONAL THEORY; DNA BINDING; GENETIC ENGINEERING AND GENE TECHNOLOGY; HYDRODYNAMICS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; QUANTUM MECHANICS; RELAXATION TIME; SHEAR FLOW; SHEAR RATE; SIMULATION; STRETCHING; VELOCITY;

EID: 33947516000     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/18/13/135702     Document Type: Article

References (27)

1. Shaqfeh E S G 2005 The dynamics of single-molecule DNA in flow J. Non-Newtownian Fluid Mech. 130 1-28
2. Perkins T T, Quake S R, Smith D E and Chu S 1994 Relaxation of a single DNA molecule observed via optical microscopy Science 264 822-5
3. LeDuc P, Harber C, Bao G and Wirtz D 1999 Dynamics of individual flexible polymers in a shear flow Nature 399 564-6
4. Doyle P S, Ladoux B and Viouvy J L 2000 Dynamics of a tethered polymer in shear flow Phys. Rev. Lett. 84 4769-72
5. Hur J S, Shaqfeh E S G and Larson R G 2000 Brownian dynamics simulations of single DNA molecules in shear flow J. Rheol. 44 713
6. Edelstein R L, Tamanaha C R, Paul P E, Miller M M, Baselt D R, Whitman L J and Colton R J 2000 The BARC biosensor applied to the detection of biological warfare agents Biosensors Bioelectron. 14 805-13
7. Brooks B R, Bruccoleri R E, Olafson B D, States D J, Swaminathan S and Karplus M 1983 CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217
8. MacKerel A D Jr, Brooks B R, Nilsson L, Roux B, Won Y and Karplus M 1998 CHARMM: the energy function and its parameterization with an overview of the program The Encyclopedia of Computational Chemistry vol 1 ed P V R Schleyer et al (Chichester: Wiley) pp 271-7
9. Wang G M and Sandberg W C 2007 at press
10. Zhang L, Goddard W A III and Jiang S 2002 Molecular simulation study of the c(4 × 2) superlattice structure of alkanethiol self-assembled monolayers on Au(111) J. Chem. Phys. 117 7342
11. Leng Y, Krstic P S, Wells J C, Cummings P T and Dean D J 2005 Interaction between benzenedithiolate and gold: classical force field for chemical bonding J. Chem. Phys. 122 244721
12. Krüger D, Fuchs H, Rousseau R, Marx D and Parrinello M 2001 Interaction of short-chain alkane thiols and thiolates with small gold clusters: adsorption structures and energetics J. Chem. Phys. 115 4776
13. Rappé A K, Casewit C J, Colwell K S, Goddard W A III and Skiff W M 1992 UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations J. Am. Chem. Soc. 114 10024-35
14. Lincoln R C, Koliwad K M and Ghate P B 1967 Morse-potential evaluation of second- and third-order elastic constants of some cubic metals Phys. Rev. 157 463
15. Mark P and Nilsson L 2002 Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations J. Comput. Chem. 23 1211-9
16. Evans D J and Morriss G P 1984 Nonlinear-response theory for steady planar Couette flow Phys. Rev. A 30 1528
17. Evans D J and Morris G P 1990 Statistical Mechanics of Nonequilibrium Liquids (London: Academic)
18. Khare R, de Pablo J J and Yethiraj A 1996 Rheology of confined polymer melts Micromolecules 29 7910
19. Sandberg W C and Heyes D M 1995 Self-diffusion in equilibrium and sheared liquid mixtures by molecular dynamics Mol. Phys. 85 635-49
20. Heyes D M 1986 Some physical consequences of large shear rates on simple fluids J. Chem. Phys. 85 997
21. Heyes D M 1997 The Liquid State: Applications of Molecular Simulations (Chichester: Wiley)
22. Sandberg W C, Obeysekare U, Williams C and Qasba A 1997 Visualization of shear-induced orientation in atomic liquids Phys. Chem. Liquids 35 67-80
23. Kim D and Darve E 2006 Molecular dynamics simulation of electro-osmotic flows in rough wall nanochannels Phys. Rev. E 73 051203
24. Khare R, de Pablo J J and Yethiraj A 1997 Molecular simulation and continuum mechanics study of simple fluids in non-isothermal planar coquette flows J. Chem. Phys. 107 2589
25. Wang G M, Sandberg W C and Kenny S D 2006 Density functional study of a typical thiol tethered on gold surface: ruptures under normal or parallel stretch Nanotechnology 17 4819-24
26. Hatfield J W and Quake S R 1999 Dynamic properties of an extended polymer in solution Phys. Rev. Lett. 82 3548
27. Chung Y-C, Lin Y-C, Hsu Y-L, Chang W-N T and Shiu M-Z 2004 The effect of velocity and extensional strain rate on enhancing DNA hybridization J. Micromech. Microeng. 14 1376-83