-
1
-
-
53649108801
-
The potential and challenges of nanopore sequencing
-
Branton, D., Deamer, D., Marziali, A., Bayley, H., Benner, S., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X., et al. (2008) The potential and challenges of nanopore sequencing Nature Biotech 26, 1146–1153.
-
(2008)
Nature Biotech
, vol.26
, pp. 1146-1153
-
-
Branton, D.1
Deamer, D.2
Marziali, A.3
Bayley, H.4
Benner, S.5
Butler, T.6
Di Ventra, M.7
Garaj, S.8
Hibbs, A.9
Huang, X.10
-
2
-
-
33646400831
-
-
Lagerqvist, J., Zwolak, M., and Ventra, M. D. (2006) Fast DNA Sequencing via Transverse Electronic Transport Nano Lett 6, 779–782.
-
(2006)
Fast DNA Sequencing via Transverse Electronic Transport Nano Lett
, vol.6
, pp. 779-782
-
-
Lagerqvist, J.1
Zwolak, M.2
Ventra, M.D.3
-
3
-
-
38749105770
-
Detection of DNA sequence using an alternating electric field in a nanopore capacitor
-
Sigalov, G., Comer, J., Timp, G., and Aksimentiev, A. (2008) Detection of DNA sequence using an alternating electric field in a nanopore capacitor Nano Lett 8, 56–63.
-
(2008)
Nano Lett
, vol.8
, pp. 56-63
-
-
Sigalov, G.1
Comer, J.2
Timp, G.3
Aksimentiev, A.4
-
4
-
-
35648963025
-
Progress toward ultrafast DNA sequencing using solid-state nanopores
-
Soni, G. V. and Meller, A. (2007) Progress toward ultrafast DNA sequencing using solid-state nanopores Clinical Chemistry 53, 1996–2001.
-
(2007)
Clinical Chemistry
, vol.53
, pp. 1996-2001
-
-
Soni, G.V.1
Meller, A.2
-
5
-
-
0036929209
-
A Fast in Silico Simulation of Ion Flux through the Large-Pore Channel Proteins
-
Bransburg-Zabary, S., Nachliel, E., and Gutman, M. (2002) A Fast in Silico Simulation of Ion Flux through the Large-Pore Channel Proteins Biophys J 83, 3001–3011.
-
(2002)
Biophys J
, vol.83
, pp. 3001-3011
-
-
Bransburg-Zabary, S.1
Nachliel, E.2
Gutman, M.3
-
6
-
-
4444234147
-
Microscopic kinetics of DNA translocation through synthetic nanopores
-
Aksimentiev, A., Heng, J. B., Timp, G., and Schulten, K. (2004) Microscopic kinetics of DNA translocation through synthetic nanopores Biophys J 87, 2086–2097.
-
(2004)
Biophys J
, vol.87
, pp. 2086-2097
-
-
Aksimentiev, A.1
Heng, J.B.2
Timp, G.3
Schulten, K.4
-
7
-
-
22244445788
-
Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map
-
Aksimentiev, A. and Schulten, K. (2005) Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map Biophys J 88, 3745–3761.
-
(2005)
Biophys J
, vol.88
, pp. 3745-3761
-
-
Aksimentiev, A.1
Schulten, K.2
-
8
-
-
50849102996
-
Electro-osmotic screening of the dna charge in a nanopore
-
Luan, B. and Aksimentiev, A. (2008) Electro-osmotic screening of the dna charge in a nanopore Phys Rev E 78, 021912.
-
(2008)
Phys Rev E
, vol.78
-
-
Luan, B.1
Aksimentiev, A.2
-
9
-
-
67651171449
-
Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore
-
Dorvel, B., Sigalov, G., Zhao, Q., Comer, J., Dimitrov, V., Mirsaidov, U., Aksimentiev, A., and Timp, G. (2009) Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore Nucl Acids Res 37, 4170–4179.
-
(2009)
Nucl Acids Res
, vol.37
, pp. 4170-4179
-
-
Dorvel, B.1
Sigalov, G.2
Zhao, Q.3
Comer, J.4
Dimitrov, V.5
Mirsaidov, U.6
Aksimentiev, A.7
Timp, G.8
-
10
-
-
34848830419
-
Exploring transmembrane transport through a-hemolysin with grid-steered molecular dynamics
-
Wells, D. B., Abramkina, V., and Aksimentiev, A. (2007) Exploring transmembrane transport through a-hemolysin with grid-steered molecular dynamics J Chem Phys 127, 125101.
-
(2007)
J Chem Phys
, vol.127
-
-
Wells, D.B.1
Abramkina, V.2
Aksimentiev, A.3
-
11
-
-
85139097177
-
-
VMD User Guide. URL: http://www.ks.uiuc. edu/Research/vmd/current/ug/ug.html.
-
VMD User Guide. URL: http://www.ks.uiuc. edu/Research/vmd/current/ug/ug.html.
-
-
-
-
12
-
-
85139174379
-
-
VMD Tutorial. URL: http://www.ks.uiuc. edu/Trai ni ng/Tutori al s/vmd/tutori al-html/index.html.
-
VMD Tutorial. URL: http://www.ks.uiuc. edu/Trai ni ng/Tutori al s/vmd/tutori al-html/index.html.
-
-
-
-
13
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD J Comp Chem 26, 1781–1802.
-
(2005)
J Comp Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
14
-
-
85139088506
-
-
NAMD User Guide. URL: http://www. ks.uiuc.edu/Research/namd/current/ug/.
-
NAMD User Guide. URL: http://www. ks.uiuc.edu/Research/namd/current/ug/.
-
-
-
-
15
-
-
85139147728
-
-
NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-unix-html/index.html.
-
NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-unix-html/index.html.
-
-
-
-
16
-
-
85139133129
-
-
NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-win-html/index.html.
-
NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-win-html/index.html.
-
-
-
-
17
-
-
67849110013
-
3D-DART: A DNA structure modelling server
-
van Dijk, M. and Bonvin, A. M. J. J. (2009) 3D-DART: a DNA structure modelling server Nucl Acids Res 37, W235–W239.
-
(2009)
Nucl Acids Res
, vol.37
, pp. W235-W239
-
-
van Dijk, M.1
Bonvin, A.M.J.J.2
-
18
-
-
58849087632
-
Microscopic mechanics of hairpin DNA translocation through synthetic nanopores
-
Comer, J., Dimitrov, V., Zhao, Q., Timp, G., and Aksimentiev, A. (2009) Microscopic mechanics of hairpin DNA translocation through synthetic nanopores Biophys J 96, 593–608.
-
(2009)
Biophys J
, vol.96
, pp. 593-608
-
-
Comer, J.1
Dimitrov, V.2
Zhao, Q.3
Timp, G.4
Aksimentiev, A.5
-
19
-
-
33645542434
-
The electromechanics of DNA in a synthetic nanopore
-
Heng, J. B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y. V., Sligar, S., Schulten, K., and Timp, G. (2006) The electromechanics of DNA in a synthetic nanopore Biophys J 90, 1098–1106.
-
(2006)
Biophys J
, vol.90
, pp. 1098-1106
-
-
Heng, J.B.1
Aksimentiev, A.2
Ho, C.3
Marks, P.4
Grinkova, Y.V.5
Sligar, S.6
Schulten, K.7
Timp, G.8
-
21
-
-
33751266937
-
Water-silica force field for simulating nanodevices
-
Cruz-Chu, E. R., Aksimentiev, A., and Schulten, K. (2006) Water-silica force field for simulating nanodevices J Phys Chem B 110, 21497–21508.
-
(2006)
J Phys Chem B
, vol.110
, pp. 21497-21508
-
-
Cruz-Chu, E.R.1
Aksimentiev, A.2
Schulten, K.3
-
22
-
-
65649150349
-
Modeling transport through synthetic nanopores
-
Aksimentiev, A., Brunner, R., Cruz-Chu, E. R., Comer, J., and Schulten, K. (2009) Modeling transport through synthetic nanopores IEEE Nanotechnology Magazine 3, 20–28.
-
(2009)
IEEE Nanotechnology Magazine
, vol.3
, pp. 20-28
-
-
Aksimentiev, A.1
Brunner, R.2
Cruz-Chu, E.R.3
Comer, J.4
Schulten, K.5
-
23
-
-
11944254490
-
Force fields for silicas and aluminophosphates based on ab initio calculations
-
van Beest, B. W. H., Kramer, G. J., and van Santen, R. A. (1990) Force fields for silicas and aluminophosphates based on ab initio calculations Phys Rev Lett 64, 1955–1958.
-
(1990)
Phys Rev Lett
, vol.64
, pp. 1955-1958
-
-
van Beest, B.W.H.1
Kramer, G.J.2
van Santen, R.A.3
-
24
-
-
0001497255
-
Cooling-rate effects in amorphous silica: A computer-simulation study
-
Vollmayr, K., Kob, W., and Binder, K. (1996) Cooling-rate effects in amorphous silica: A computer-simulation study Phys Rev B 54, 15808–15827.
-
(1996)
Phys Rev B
, vol.54
, pp. 15808-15827
-
-
Vollmayr, K.1
Kob, W.2
Binder, K.3
-
25
-
-
65349156366
-
Ionic current rectification through silica nanopores
-
Cruz-Chu, E. R., Aksimentiev, A., and Schulten, K. (2009) Ionic current rectification through silica nanopores J Phys Chem C 113, 1850–1862.
-
(2009)
J Phys Chem C
, vol.113
, pp. 1850-1862
-
-
Cruz-Chu, E.R.1
Aksimentiev, A.2
Schulten, K.3
-
26
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
-
Grubmüller, H., Heymann, B., and Tavan, P. (1996) Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force Science 271, 997–999.
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmüller, H.1
Heymann, B.2
Tavan, P.3
-
27
-
-
1542289939
-
Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase
-
Aksimentiev, A., Balabin, I. A., Fillingame, R. H., and Schulten, K. (2004) Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase Biophys J 86, 1332–1344.
-
(2004)
Biophys J
, vol.86
, pp. 1332-1344
-
-
Aksimentiev, A.1
Balabin, I.A.2
Fillingame, R.H.3
Schulten, K.4
-
28
-
-
23044471060
-
Electrolytic transport through a synthetic nanometer-diameter pore
-
Ho, C., Qiao, R., Chatterjee, A., Timp, R. J., Aluru, N. R., and Timp, G. (2005) Electrolytic transport through a synthetic nanometer-diameter pore Proc Natl Acad Sci USA 102, 10445–14450.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10445-14450
-
-
Ho, C.1
Qiao, R.2
Chatterjee, A.3
Timp, R.J.4
Aluru, N.R.5
Timp, G.6
-
29
-
-
34247494251
-
Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope
-
Kim, M., McNally, B., Murata, K., and Meller, A. (2007) Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope Nanotechnology 18, 205302.
-
(2007)
Nanotechnology
, vol.18
-
-
Kim, M.1
McNally, B.2
Murata, K.3
Meller, A.4
-
30
-
-
0032762996
-
Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and poly-uridylic acid as homopolymers or as segments within singe RNA molecules
-
Akeson, M., Branton, D., Kasianowicz, J. J., Brandin, E., and Deamer, D. W. (1999) Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and poly-uridylic acid as homopolymers or as segments within singe RNA molecules Biophys J 77, 3227–3233.
-
(1999)
Biophys J
, vol.77
, pp. 3227-3233
-
-
Akeson, M.1
Branton, D.2
Kasianowicz, J.J.3
Brandin, E.4
Deamer, D.W.5
-
31
-
-
0033980542
-
Rapid nanopore discrimination between single polynucleotide molecules
-
Meller, A., Nivon, L., Brandin, E., Golovchenko, J., and Branton, D. (2000) Rapid nanopore discrimination between single polynucleotide molecules Proc Natl Acad Sci USA 97, 1079–1084.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 1079-1084
-
-
Meller, A.1
Nivon, L.2
Brandin, E.3
Golovchenko, J.4
Branton, D.5
-
32
-
-
0035107270
-
Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel
-
Vercoutere, W., Winters-Hilt, S., Olsen, H., Deamer, D., Haussler, D., and Akeson, M. (2001) Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel Nature Biotech 19, 248–252.
-
(2001)
Nature Biotech
, vol.19
, pp. 248-252
-
-
Vercoutere, W.1
Winters-Hilt, S.2
Olsen, H.3
Deamer, D.4
Haussler, D.5
Akeson, M.6
-
33
-
-
0037440660
-
Discrimination among individual Watson-Crick base pairs at the ter- mini of single DNA hairpin molecules
-
Vercoutere, W. A., Winters-Hilt, S., DeGuzman, V. S., Deamer, D., Ridino, S. E., Rodgers, J. T., Olsen, H. E., Marziali, A., and Akeson, M. (2003) Discrimination among individual Watson-Crick base pairs at the ter- mini of single DNA hairpin molecules Nucl Acids Res 31, 1311–1318.
-
(2003)
Nucl Acids Res
, vol.31
, pp. 1311-1318
-
-
Vercoutere, W.A.1
Winters-Hilt, S.2
Deguzman, V.S.3
Deamer, D.4
Ridino, S.E.5
Rodgers, J.T.6
Olsen, H.E.7
Marziali, A.8
Akeson, M.9
-
34
-
-
3042736845
-
A nanosensor for transmembrane capture and identification of single nucleic acid molecules
-
Nakane, J., Wiggin, M., and Marziali, A. (2004) A nanosensor for transmembrane capture and identification of single nucleic acid molecules Biophys J 87, 615–621.
-
(2004)
Biophys J
, vol.87
, pp. 615-621
-
-
Nakane, J.1
Wiggin, M.2
Marziali, A.3
-
35
-
-
14844290867
-
Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores
-
Ashkenasy, N., Sánchez-Quesada, J., Bayley, H., and Ghadiri, M. R. (2005) Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores Angew Chem Int Ed Engl 44, 1401–1404.
-
(2005)
Angew Chem Int Ed Engl
, vol.44
, pp. 1401-1404
-
-
Ashkenasy, N.1
Sánchez-Quesada, J.2
Bayley, H.3
Ghadiri, M.R.4
-
36
-
-
31044443423
-
Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor
-
Gracheva, M. E., Xiong, A., Leburton, J.-P., Aksimentiev, A., Schulten, K., and Timp, G. (2006) Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor Nanotechnology 17, 622–633.
-
(2006)
Nanotechnology
, vol.17
, pp. 622-633
-
-
Gracheva, M.E.1
Xiong, A.2
Leburton, J.-P.3
Aksimentiev, A.4
Schulten, K.5
Timp, G.6
-
37
-
-
33746625243
-
Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor
-
Gracheva, M. E., Aksimentiev, A., and Leburton, J.-P. (2006) Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor Nanotechnology 17, 3160–3165.
-
(2006)
Nanotechnology
, vol.17
, pp. 3160-3165
-
-
Gracheva, M.E.1
Aksimentiev, A.2
Leburton, J.-P.3
-
38
-
-
38349169632
-
A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution
-
Cockroft, S., Chu, J., Amorin, M., and Ghadiri, M. (2008) A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution J Am Chem Soc 130, 818–820.
-
(2008)
J am Chem Soc
, vol.130
, pp. 818-820
-
-
Cockroft, S.1
Chu, J.2
Amorin, M.3
Ghadiri, M.4
-
39
-
-
0030465241
-
Characterization of individual polynucleotide molecules using a membrane channel
-
Kasianowicz, J. J., Brandin, E., Branton, D., and Deamer, D. W. (1996) Characterization of individual polynucleotide molecules using a membrane channel Proc Natl Acad Sci USA 93, 13770–13773.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 13770-13773
-
-
Kasianowicz, J.J.1
Brandin, E.2
Branton, D.3
Deamer, D.W.4
-
41
-
-
24644451580
-
Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel
-
Mathé, J., Aksimentiev, A., Nelson, D. R., Schulten, K., and Meller, A. (2005) Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel Proc Natl Acad Sci USA 102, 12377–12382.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12377-12382
-
-
Mathé, J.1
Aksimentiev, A.2
Nelson, D.R.3
Schulten, K.4
Meller, A.5
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