A long DNA segment in a linear nanoscale Paul trap

Nanotechnology

Volumn 21, Issue 1, 2010, Pages

  Joseph, Sony ^a   Guan, Weihua ^b   Reed, Mark A ^b   Krstic, Predrag S ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AXIAL DIRECTION; CENTER OF MASS; CHARGE-TO-MASS RATIOS; DNA SEGMENTS; IN-VACUUM; INITIAL ANGLE; LINE CHARGES; MOLECULAR DYNAMICS SIMULATIONS; NANO SCALE; PAUL TRAP; SINGLE ION; SINGLE-STRANDED DNA; SINGLE-STRANDED DNA (SS-DNA); STABILITY PARAMETERS; STABILITY REGIONS; TRAP PARAMETERS; VARIABLE LENGTH;

DNA; GENES; MOLECULAR DYNAMICS; NANOSTRUCTURED MATERIALS; NUCLEIC ACIDS;

ROTATION;

NANOBEAD; SINGLE STRANDED DNA; MICROSPHERE;

ARTICLE; DNA DETERMINATION; ION TRAP MASS SPECTROMETRY; LINEAR NANOSCALE PAUL TRAP; MOLECULAR DYNAMICS; NANOANALYSIS; OSCILLATION; PRIORITY JOURNAL; PROTEIN STABILITY; ROTATION; SIMULATION; VACUUM; CHEMISTRY; CONFORMATION; KINETICS; NANOTECHNOLOGY; PARTICLE SIZE; PLIABILITY; TIME;

DNA, SINGLE-STRANDED; KINETICS; MICROSPHERES; MOLECULAR DYNAMICS SIMULATION; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; PARTICLE SIZE; PLIABILITY; TIME FACTORS;

EID: 71549171457     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/21/1/015103     Document Type: Article

References (45)

1. Abich K, Keil A, Reiss D, Wunderlich C, Neuhauser W and Toschek P E 2004 Thermally activated hopping of two ions trapped in a bistable potential well J. Opt. A: Pure Appl. Opt. B 6 S18-23
2. Aksimentiev A, Heng J B, Timp G and Schulten K 2004a Microscopic kinetics of DNA translocation through synthetic nanopores Biophys. J. 87 2086-97
3. Aksimentiev A, Schulten K, Heng J, Ho C and Timp G 2004b Molecular dynamics simulations of a nanopore device for DNA sequencing Biophys. J. 86 480A-A
4. Arnott D, Henzel W J and Stults J T 1998 Rapid identification of comigrating gel-isolated proteins by ion trap mass spectrometry Electrophoresis 19 968-80
5. Branton D et al 2008 The potential and challenges of nanopore sequencing Nat. Biotechnol. 26 146-53
6. Bussi G, Donadio D and Parrinello M 2007 Canonical sampling through velocity rescaling J. Chem. Phys. 126 014101
7. Chen C M 2005 Driven translocation dynamics of polynucleotides through a nanopore: off-lattice Monte Carlo simulations Physica A 350 95-107
8. Chen C M and Peng E H 2003 Nanopore sequencing of polynucleotides assisted by a rotating electric field Appl. Phys. Lett. 82 1308-10
9. Duan Y et al 2003 A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24 1999-2012
10. + Appl. Phys. B 59 179-85
11. Fredlake C P, Hert D G, Mardis E R and Barron A E 2006 What is the future of electrophoresis in large-scale genomic sequencing? Electrophoresis 27 3689-702
12. Healy K 2007 Nanopore-based single-molecule DNA analysis Nanomedicine 2 459-81
13. Hess B, Kutzner C, vander Spoel D and Lindahl E 2008 GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 435-47
14. Hoffnagle J J and Brewer R G 1994 Science 265 213
15. Howorka S, Cheley S S and Bayley H 2001 Nat. Biotechnol. 19 636
16. Humphrey W, Dalke A and Schulten K 1996 VMD: visual molecular dynamics J. Mol. Graphics 14 33
17. Itano W M, Bergquist J C, Bollinger J J and Wineland D J 1995 Cooling methods in ion traps Phys. Scr. T 59 106-20
18. Kasianowicz J J, Brandin E, Branton D and Deamer D W 1996 Proc. Natl Acad. Sci. USA 93 13770
19. Kricka L J, Park J Y, Li S F Y and Fortina P 2005 Miniaturized detection technology in molecular diagnostics Expert Rev. Mol. Diagnos. 5 549-59
20. Lagerqvist J, Zwolak M and Di Ventra M 2006 Fast DNA sequencing via transverse electronic transport Nano Lett. 6 779
21. Lagerqvist J, Zwolak M and Di Ventra M 2007 Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport Biophys. J. 93 2384-90
22. Leibfried D, Blatt R, Monroe C and Wineland D 2003 Quantum dynamics of single trapped ions Rev. Mod. Phys. 75 281-324 (Pubitemid 36539842)
23. Nakane J J, Akeson M and Marziali A 2003 Nanopore sensors for nucleic acid analysis J. Phys.: Condens. Matter 15 R1365-93
24. Oberacher H, Parson W, Oefner P J, Mayr B M and Huber C G 2004 Applicability of tandem mass spectrometry to the automated comparative sequencing of long-chain oligonucleotides J. Am. Soc. Mass Spectrometry 15 510-22
25. Paul W 1990 Electromagnetic traps for charged and neutral particles Rev. Mod. Phys. 62 531-40
26. Payne C M, Zhao X C, Vlcek L and Cummings P T 2008 Molecular dynamics simulation of ss-DNA translocation between a copper nanoelectrode gap incorporating electrode charge dynamics J. Phys. Chem. B 112 1712-7
27. Rhee M and Burns M A 2006 Nanopore sequencing technology: research trends and applications Trends Biotechnol. 24 580-6
28. Rhee M and Burns M A 2007 Nanopore sequencing technology: nanopore preparations Trends Biotechnol. 25 174-81
29. Rothbauer U, Zolghadr K, Muyldermans S, Schepers A, Cardoso M C and Leonhardt H 2008 A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins Mol. Cell. Proteomics 7 282-9
30. Ryan D, Rahimi M, Lund J, Mehta R and Parviz B A 2007 Toward nanoscale genome sequencing Trends Biotechnol. 25 385-9
31. Schiffer J P 2003 Order in confined ions J. Physique B 36 511-23
32. Seidelin S et al 2006 Microfabricated surface-electrode ion trap for scalable quantum information processing Phys. Rev. Lett. 96 253003
33. Shi L, Zhu X W, Feng M and Fang X M 1999 Ordered structures of a few ions in the Paul trap Commun. Theor. Phys. 31 491-6
34. Sorin E J and Pande V S 2005 Exploring the helix-coil transition via all-atom equilibrium ensemble simulations Biophys. J. 88 2472-93
35. Tabard-Cossa V, Trivedi D, Wiggin M, Jetha N N and Marziali A 2007 Noise analysis and reduction in solid-state nanopores Nanotechnology 18 305505
36. Trepagnier E H, Radenovic A, Sivak D, Geissler P and Liphardt J 2007 Controlling DNA capture and propagation through artificial nanopores Nano Lett. 7 2824-30
37. Tsai Y S and Chen C M 2007 Driven polymer transport through a nanopore controlled by a rotating electric field: off-lattice computer simulations J. Chem. Phys. 126 144910
38. Vant K, Chiaverini J, Lybarger W and Berkeland D J 2006 Photoionization of strontium for trapped-ion quantum information processing arXiv:quant-ph/ 0607055
39. Walther H 1995 From a single-ion to a mesoscopic system-crystallization of ions in Paul traps Phys. Scr. T 59 360-8
40. Wineland D J, Monroe C, Itano W M, Leibfried D, King B E and Meekhof D M 1998 Experimental issues in coherent quantum-state manipulation of trapped atomic ions J. Res. Natl Inst. Standards Technol. 103 259-328
41. Zhang X G, Krstic P S, Zikic R, Wells J C and Fuentes-Cabrera M 2006 First-principles transversal DNA conductance deconstructed Biophys. J. 91 L4-6
42. Zhao X C and Krstic P S 2008 Molecular dynamics simulation study on trapping ions in a nanoscale Paul trap Nanotechnology 19 195702
43. Zhao X C, Payne C M, Cummings P T and Lee J W 2007 Single-strand DNA molecule translocation through nanoelectrode gaps Nanotechnology 18 424018
44. Zikic R, Krstic P S, Zhang X G, Fuentes-Cabrera M, Wells J and Zhao X C 2006 Characterization of the tunneling conductance across DNA bases Phys. Rev. E 74 011916
45. Zwolak M and Di Ventra M 2005 Electronic signature of DNA nucleotides via transverse transport Nano Lett. 5 421