-
2
-
-
33644504834
-
DNA conformation on surfaces measured by fluorescence self-interference
-
Moiseev L, Unlu S, Swan A K, Goldberg B B and Cantor C R 2006 DNA conformation on surfaces measured by fluorescence self-interference Proc. Natl Acad. Sci. 103 2623-8
-
(2006)
Proc. Natl Acad. Sci.
, vol.103
, Issue.8
, pp. 2623-2628
-
-
Moiseev, L.1
Unlu, S.2
Swan, A.K.3
Goldberg, B.B.4
Cantor, C.R.5
-
3
-
-
11644292504
-
Orienting DNA helices on gold using applied electric fields
-
Kelley S O, Barton J K, Jackson N M, McPherson L D, Potter A B, Spain E M, Allen M J and Hill M G 1998 Orienting DNA helices on gold using applied electric fields Langmuir 14 6781-4
-
(1998)
Langmuir
, vol.14
, Issue.24
, pp. 6781-6784
-
-
Kelley, S.O.1
Barton, J.K.2
Jackson, N.M.3
McPherson, L.D.4
Potter, A.B.5
Spain, E.M.6
Allen, M.J.7
Hill, M.G.8
-
4
-
-
47949123944
-
Structural and optical properties of DNA layers covalently attached to diamond surfaces
-
Wenmackers S et al 2008 Structural and optical properties of DNA layers covalently attached to diamond surfaces Langmuir 24 7269-77
-
(2008)
Langmuir
, vol.24
, Issue.14
, pp. 7269-7277
-
-
Wenmackers, S.1
-
5
-
-
85076080303
-
Theoretical considerations for the efficient design of DNA arrays
-
(Mechanical Engineering Series) ed J E Moore Jr and G Zouridakis (Boca Raton, FL: CRC Press)
-
Vainrub A, Li T B, Fofanov Y and Pettitt B M 2003 Theoretical considerations for the efficient design of DNA arrays Biomedical Technology and Devices Handbook (Mechanical Engineering Series) ed J E Moore Jr and G Zouridakis (Boca Raton, FL: CRC Press) 14:1-12
-
(2003)
Biomedical Technology and Devices Handbook
-
-
Vainrub, A.1
Li, T.B.2
Fofanov, Y.3
Pettitt, B.M.4
-
6
-
-
35248891626
-
Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration
-
Jayaraman A, Hall C and Genzer J 2007 Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration J. Chem. Phys. 127 144912
-
(2007)
J. Chem. Phys.
, vol.127
, Issue.14
, pp. 144912
-
-
Jayaraman, A.1
Hall, C.2
Genzer, J.3
-
7
-
-
2542503495
-
Static and dynamic properties of tethered chains at adsorbing surfaces: A Monte Carlo study
-
Descas R, Sommer J U and Blumen A 2004 Static and dynamic properties of tethered chains at adsorbing surfaces: a Monte Carlo study J. Chem. Phys. 120 8831-40
-
(2004)
J. Chem. Phys.
, vol.120
, Issue.18
, pp. 8831-8840
-
-
Descas, R.1
Sommer, J.U.2
Blumen, A.3
-
8
-
-
0035588097
-
A study of DNA tethered to a surface by an all-atom molecular dynamics simulation
-
Wong K and Pettitt B M 2001 A study of DNA tethered to a surface by an all-atom molecular dynamics simulation Theor. Chem. Acc. 106 233-5
-
(2001)
Theor. Chem. Acc.
, vol.106
, pp. 233-235
-
-
Wong, K.1
Pettitt, B.M.2
-
9
-
-
1842632558
-
Orientation of DNA on a Surface from Simulation
-
DOI 10.1002/bip.20004
-
Wong K and Pettitt B M 2004 Orientation of DNA on a surface from simulation Biopolymers 73 570-8 (Pubitemid 38480704)
-
(2004)
Biopolymers
, vol.73
, Issue.5
, pp. 570-578
-
-
Wong, K.-Y.1
Pettitt, B.M.2
-
10
-
-
62749194584
-
The melting mechanism of DNA tethered to a surface
-
Qamhieh K, Wong K, Lynch G and Pettitt B M 2009 The melting mechanism of DNA tethered to a surface IJNAM 6 474-88
-
(2009)
IJNAM
, vol.6
, pp. 474-488
-
-
Qamhieh, K.1
Wong, K.2
Lynch, G.3
Pettitt, B.M.4
-
11
-
-
70349143774
-
Interaction between DNAs on a gold surface
-
Lee O and Schatz G C 2009 Interaction between DNAs on a gold surface J. Phys. Chem. C 113 15941-7
-
(2009)
J. Phys. Chem.
, vol.113
, Issue.36
, pp. 15941-15947
-
-
Lee, O.1
Schatz, G.C.2
-
12
-
-
36348981525
-
Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): A molecular simulation study
-
Yao L, Sullivan J, Hower J, He Y and Jiang S 2007 Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study J. Chem. Phys. 127 195101
-
(2007)
J. Chem. Phys.
, vol.127
, Issue.19
, pp. 195101
-
-
Yao, L.1
Sullivan, J.2
Hower, J.3
He, Y.4
Jiang, S.5
-
14
-
-
77957903935
-
A model for stucture and thermodynamics of ss DNA and ds DNA near a surface: A coarse grained approach
-
Ambia-Garrido J, Vainrub A and Pettitt B M 2010 A model for stucture and thermodynamics of ss DNA and ds DNA near a surface: a coarse grained approach Comput. Phys. Commun. 181 2001-7
-
(2010)
Comput. Phys. Commun.
, vol.181
, Issue.12
, pp. 2001-2007
-
-
Ambia-Garrido, J.1
Vainrub, A.2
Pettitt, B.M.3
-
15
-
-
0001232644
-
Thermodynamics of association to a molecule immobilized in an electric double layer
-
Vainrub A and Pettitt B M 2000 Thermodynamics of association to a molecule immobilized in an electric double layer Chem. Phys. Lett. 323 160-6
-
(2000)
Chem. Phys. Lett.
, vol.323
, Issue.1-2
, pp. 160-166
-
-
Vainrub, A.1
Pettitt, B.M.2
-
16
-
-
85036155972
-
Coulomb blockage of hybridization in two-dimensional DNA arrays
-
Vainrub A and Pettitt B M 2002 Coulomb blockage of hybridization in two-dimensional DNA arrays Phys. Rev. E 66 041905
-
(2002)
Phys. Rev.
, vol.66
, Issue.4
, pp. 041905
-
-
Vainrub, A.1
Pettitt, B.M.2
-
17
-
-
0037527767
-
Sensitive quantitative nucleic acid detection using oligonucleotide microarrays
-
DOI 10.1021/ja035020q
-
Vainrub A and Pettitt B M 2003 Sensitive quantitative nucleic acid detection using oligonucleotide microarrays J. Am. Chem. Soc. 125 7798-9 (Pubitemid 36782146)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.26
, pp. 7798-7799
-
-
Vainrub, A.1
Pettitt, B.M.2
-
18
-
-
0026495432
-
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
-
Smith S B, Finzi L and Bustamante C 1992 Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads Science 258 1122-6
-
(1992)
Science
, vol.258
, Issue.5085
, pp. 1122-1126
-
-
Smith, S.B.1
Finzi, L.2
Bustamante, C.3
-
20
-
-
85015087906
-
Ten years of tension: Single-molecule DNA mechanics
-
DOI 10.1038/nature01405
-
Bustamante C, Bryant Z and Smith S B 2003 Ten years of tension: single-molecule DNA mechanics Nature 421 423-7 (Pubitemid 36157948)
-
(2003)
Nature
, vol.421
, Issue.6921
, pp. 423-427
-
-
Bustamante, C.1
Bryant, Z.2
Smith, S.B.3
-
21
-
-
1942423138
-
Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy
-
Murphy M C, Rasnik I, Cheng W, Lohman T M and Ha T 2004 Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy Biophys. J. 86 2530-7 (Pubitemid 38524439)
-
(2004)
Biophysical Journal
, vol.86
, Issue.4
, pp. 2530-2537
-
-
Murphy, M.C.1
Rasnik, I.2
Cheng, W.3
Lohman, T.M.4
Ha, T.5
-
22
-
-
0031238076
-
Persistence length of single-stranded DNA
-
Tinland B, Pluen A, Sturm J and Weill G 1997 Persistence length of single-stranded DNA Macromolecules 30 5763-5 (Pubitemid 127592220)
-
(1997)
Macromolecules
, vol.30
, Issue.19
, pp. 5763-5765
-
-
Tinland, B.1
Pluen, A.2
Sturm, J.3
Weill, G.4
-
23
-
-
61849131735
-
Persistence length of short-chain branched polyethylene
-
Ramachandran R, Beaucage G, Kulkarni A, McFaddin D, Merrick-Mack J and Galiatsatos V 2008 Persistence length of short-chain branched polyethylene Macromolecules 41 9802-6
-
(2008)
Macromolecules
, vol.41
, Issue.24
, pp. 9802-9806
-
-
Ramachandran, R.1
Beaucage, G.2
Kulkarni, A.3
McFaddin, D.4
Merrick-Mack, J.5
Galiatsatos, V.6
-
24
-
-
0034578683
-
The distribution of end-to-end distances of the weakly bending rod model
-
Schurr J M and Fujimoto B S 2000 The distribution of end-to-end distances of the weakly bending rod model Biopolymers 54 561-71
-
(2000)
Biopolymers
, vol.54
, Issue.7
, pp. 561-571
-
-
Schurr, J.M.1
Fujimoto, B.S.2
-
25
-
-
0000555535
-
Sur la constitution de la charge lectrique a la surface d'un lectrolyte
-
Gouy G J 1910 Sur la constitution de la charge lectrique a la surface d'un lectrolyte J. Physique. 9 457-68
-
(1910)
J. Physique.
, vol.9
, pp. 457-468
-
-
Gouy, G.J.1
-
26
-
-
0000264109
-
A contribution to the theory of electrocapilarity
-
Chapman D L 1913 A contribution to the theory of electrocapilarity Phil. Mag. 25 475-81
-
(1913)
Phil. Mag.
, vol.25
, pp. 475-481
-
-
Chapman, D.L.1
-
27
-
-
5244346308
-
Electrostatic double-layer interaction between two charged ion-penetrable spheres: An exact solvable model
-
Ohshima H and Kondo T 1993 Electrostatic double-layer interaction between two charged ion-penetrable spheres: an exact solvable model J. Colloid Interface Sci. 155 499-505
-
(1993)
J. Colloid Interface Sci.
, vol.155
, Issue.2
, pp. 499-505
-
-
Ohshima, H.1
Kondo, T.2
-
28
-
-
30244578100
-
Electrostatic interaction of an ion-penetrable sphere with a hard plate: Contribution of an image interaction
-
Ohshima H and Kondo T 1993 Electrostatic interaction of an ion-penetrable sphere with a hard plate: contribution of an image interaction J. Colloid Interface Sci. 157 504-8
-
(1993)
J. Colloid Interface Sci.
, vol.157
, Issue.2
, pp. 504-508
-
-
Ohshima, H.1
Kondo, T.2
-
29
-
-
0001202352
-
Monte carlo studies on the fleely jointed polymer chain with excluded volume interaction
-
Baumgartnet A and Binder K 1979 Monte carlo studies on the fleely jointed polymer chain with excluded volume interaction J. Chem. Phys. 71 2541-5
-
(1979)
J. Chem. Phys.
, vol.71
, Issue.6
, pp. 2541-2545
-
-
Baumgartnet, A.1
Binder, K.2
-
30
-
-
18344362394
-
On the use of classical statistical mechanics in the treatment of polymer chain conformation
-
Go N and Scheraga H A 1976 On the use of classical statistical mechanics in the treatment of polymer chain conformation Macromolecules 9 535-41
-
(1976)
Macromolecules
, vol.9
, Issue.4
, pp. 535-541
-
-
Go, N.1
Scheraga, H.A.2
-
31
-
-
0000127140
-
Method for estimating the configurational entropy of macromolecules
-
Karplus M and Kushick J N 1981 Method for estimating the configurational entropy of macromolecules Macromolecules 14 325-32
-
(1981)
Macromolecules
, vol.14
, Issue.2
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.N.2
-
32
-
-
0000961995
-
Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations of an alpha-helix
-
Levy R M, Karplus M, Kushick J and David P 1984 Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an alpha-helix Macromolecules 17 1370-4
-
(1984)
Macromolecules
, vol.17
, Issue.7
, pp. 1370-1374
-
-
Levy, R.M.1
Karplus, M.2
Kushick, J.3
David, P.4
-
33
-
-
0011146589
-
Corrections to the quasiharmonic approximation for evaluating molecular entropies
-
Rojas O L and Levy R M 1986 Corrections to the quasiharmonic approximation for evaluating molecular entropies J. Chem. Phys. 85 1037-43
-
(1986)
J. Chem. Phys.
, vol.85
, Issue.2
, pp. 1037-1043
-
-
Rojas, O.L.1
Levy, R.M.2
-
34
-
-
0023475026
-
Configurational entropy of native proteins
-
Karplus M, Ichiye T and Pettitt B M 1987 Configurational entropy of native proteins Biophys. J. 52 1083-5
-
(1987)
Biophys. J.
, vol.52
, Issue.6
, pp. 1083-1085
-
-
Karplus, M.1
Ichiye, T.2
Pettitt, B.M.3
-
35
-
-
0001351515
-
Estimation of absolute and relative entropies of macromolecules using covariance matrix
-
Schlitter J 1993 Estimation of absolute and relative entropies of macromolecules using covariance matrix Chem. Phys. Lett. 215 617-21
-
(1993)
Chem. Phys. Lett.
, vol.215
, Issue.6
, pp. 617-621
-
-
Schlitter, J.1
-
36
-
-
0000885331
-
Harmonic analysis of large systems I. Methodology
-
Brooks B R, Janezic D and Karplus M 1995 Harmonic analysis of large systems I. Methodology J. Comput. Chem. 16 1522-42
-
(1995)
J. Comput. Chem.
, vol.16
, Issue.12
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
37
-
-
0034323089
-
Absolute entropies from molecular dynamics simulation trajectories
-
DOI 10.1063/1.1309534
-
Schafer H, Mark A E and van Gunsteren W F 2000 Absolute entropies from molecular dynamics simulation trajectories J. Chem. Phys. 113 7809-17 (Pubitemid 32023177)
-
(2000)
Journal of Chemical Physics
, vol.113
, Issue.18
, pp. 7809-7817
-
-
Schafer, H.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
38
-
-
33748569797
-
Defects can increase the melting temperature of DNA-nanoparticle assemblies
-
DOI 10.1021/jp062287d
-
Harris N C and Kiang C 2006 Defects can increase the melting temperature of DNA-nanoparticle assemblies J. Phys. Chem. B 110 16393-6 (Pubitemid 44373364)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.33
, pp. 16393-16396
-
-
Harris, N.C.1
Kiang, C.-H.2
-
39
-
-
0035828630
-
On the calculation of entropy from covariance matrices of the atomic fluctuations
-
DOI 10.1063/1.1401821
-
Andricioaei I and Karplus M 2001 On the calculation of the entropy from covariance matrices of the atomic fluctuations J. Chem. Phys. 115 6289-92 (Pubitemid 33046603)
-
(2001)
Journal of Chemical Physics
, vol.115
, Issue.14
, pp. 6289-6292
-
-
Andricioaei, I.1
Karplus, M.2
-
40
-
-
36849137515
-
Monte carlo calculation of the average extension of molecular chains
-
Rosenbluth M N and Rosenbluth A W 1955 Monte carlo calculation of the average extension of molecular chains J. Chem. Phys. 23 356-9
-
(1955)
J. Chem. Phys.
, vol.23
, Issue.2
, pp. 356-359
-
-
Rosenbluth, M.N.1
Rosenbluth, A.W.2
-
41
-
-
4043180889
-
A new method for simulation of the real chains: Scanning future steps
-
Meirovitch H 1982 A new method for simulation of the real chains: scanning future steps J. Phys. A: Math. Gen. 15 L735-41
-
(1982)
J. Phys. A: Math. Gen.
, vol.15
, Issue.12
-
-
Meirovitch, H.1
-
42
-
-
0000799811
-
Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks
-
Meirovitch H 1985 Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks Phys. Rev. A 32 3699-708
-
(1985)
Phys. Rev.
, vol.32
, Issue.6
, pp. 3699-3708
-
-
Meirovitch, H.1
-
43
-
-
0001251117
-
Computer simulation of the free energy of the polymer chains with excluded volume and with finite interactions
-
Meirovitch H 1985 Computer simulation of the free energy of the polymer chains with excluded volume and with finite interactions Phys. Rev. A 32 3709-15
-
(1985)
Phys. Rev.
, vol.32
, Issue.6
, pp. 3709-3715
-
-
Meirovitch, H.1
-
44
-
-
36549091279
-
Computer simulation of long polymers adsorbed on a surface. I. Corrections to scaling in an ideal chain
-
Livine S and Meirovitch H 1988 Computer simulation of long polymers adsorbed on a surface. I. Corrections to scaling in an ideal chain J. Chem. Phys. 88 4498-506
-
(1988)
J. Chem. Phys.
, vol.88
, Issue.7
, pp. 4498-4506
-
-
Livine, S.1
Meirovitch, H.2
-
45
-
-
36549091650
-
Computer simulation of long polymers adsorbed on a surface. II. Critical behavior of a single self-avoiding walk
-
Meirovitch H and Livine S 1988 Computer simulation of long polymers adsorbed on a surface. II. Critical behavior of a single self-avoiding walk J. Chem. Phys. 88 4507-15
-
(1988)
J. Chem. Phys.
, vol.88
, Issue.7
, pp. 4507-4515
-
-
Meirovitch, H.1
Livine, S.2
-
47
-
-
33746099689
-
Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecule dynamics method
-
Cheluvaraja S and Meirovitch H 2006 Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecule dynamics method J. Chem. Phys. 125 024905
-
(2006)
J. Chem. Phys.
, vol.125
, Issue.2
, pp. 024905
-
-
Cheluvaraja, S.1
Meirovitch, H.2
-
48
-
-
76649103043
-
Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics
-
Meirovitch H 2010 Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics J. Mol. Recognit. 23 153-72
-
(2010)
J. Mol. Recognit.
, vol.23
, pp. 153-172
-
-
Meirovitch, H.1
-
49
-
-
0001559993
-
Configuration of isolated polymer molecules adsorbed on solid surface studied by monte-carlo computer simulation
-
McCrackin F L 1967 Configuration of isolated polymer molecules adsorbed on solid surface studied by monte-carlo computer simulation J. Chem. Phys. 47 1980-6
-
(1967)
J. Chem. Phys.
, vol.47
, Issue.6
, pp. 1980-1986
-
-
McCrackin, F.L.1
-
50
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch W 1976 A solution for the best rotation to relate two sets of vectors Acta Crystallogr. A 32 922-3
-
(1976)
Acta Crystallogr.
, vol.32
, Issue.5
, pp. 922-923
-
-
Kabsch, W.1
-
51
-
-
12944249776
-
A discussion of the dolution for the best rotation to relate two sets of vectors
-
Kabsch W 1978 A discussion of the dolution for the best rotation to relate two sets of vectors Acta Crystallogr. A 34 827-8
-
(1978)
Acta Crystallogr.
, vol.34
, Issue.5
, pp. 827-828
-
-
Kabsch, W.1
-
52
-
-
84975553202
-
Closed-form solution of absolute orientation using unit quaternions
-
Horn B K 1986 Closed-form solution of absolute orientation using unit quaternions J. Opt. Soc. Am. A 4 629-41
-
(1986)
J. Opt. Soc. Am.
, vol.4
, Issue.4
, pp. 629-641
-
-
Horn, B.K.1
|