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Items: 1 to 20 of 97

1.

Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium.

Chakraborty K, Mantha S, Bandyopadhyay S.

J Chem Phys. 2013 Aug 21;139(7):075103. doi: 10.1063/1.4818537.

PMID:
23968115
2.

Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies.

Chakraborty K, Khatua P, Bandyopadhyay S.

Phys Chem Chem Phys. 2016 Jun 21;18(23):15899-910. doi: 10.1039/c6cp00663a.

PMID:
27241311
3.

Correlated dynamical crossovers of the hydration layer of a single-stranded DNA oligomer.

Chakraborty K, Bandyopadhyay S.

J Phys Chem B. 2014 Jan 16;118(2):413-22. doi: 10.1021/jp408234k.

PMID:
24369105
4.
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6.

Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimer.

Stefl R, Fadrná E, Koca J.

J Biomol Struct Dyn. 1999 Apr;16(5):1087-95.

PMID:
10333178
7.

Molecular dynamics simulation of a DNA containing a single strand break.

Yamaguchi H, Siebers JG, Furukawa A, Otagiri N, Osman R.

Radiat Prot Dosimetry. 2002;99(1-4):103-8.

PMID:
12194259
8.

Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA.

Chakraborty K, Bandyopadhyay S.

J Chem Phys. 2015 Jan 7;142(1):015101. doi: 10.1063/1.4904896.

PMID:
25573583
9.

Molecular dynamics of potential rRNA binders: single-stranded nucleic acids and some analogues.

Panecka J, Mura C, Trylska J.

J Phys Chem B. 2011 Jan 27;115(3):532-46. doi: 10.1021/jp106404u.

PMID:
21192664
10.

Self-assembly of DNA on a gapped carbon nanotube.

Bobadilla AD, Seminario JM.

J Mol Model. 2012 Jul;18(7):3291-300. doi: 10.1007/s00894-011-1341-8.

PMID:
22252833
11.

Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering.

Sim AY, Lipfert J, Herschlag D, Doniach S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021901.

PMID:
23005779
13.

Direct observation of essential DNA dynamics: melting and reformation of the DNA minor groove.

Banerjee D, Pal SK.

J Phys Chem B. 2007 Sep 13;111(36):10833-8.

PMID:
17676797
14.

Dielectric dispersion of short single-stranded DNA in aqueous solutions with and without added salt.

Katsumoto Y, Omori S, Yamamoto D, Yasuda A, Asami K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jan;75(1 Pt 1):011911. Erratum in: Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jan;75(1 Pt 2):019907.

PMID:
17358188
15.

Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water.

Jana M, Bandyopadhyay S.

Phys Chem Chem Phys. 2012 May 14;14(18):6628-38. doi: 10.1039/c2cp24104h.

PMID:
22460826
16.

Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it.

Sinha SK, Bandyopadhyay S.

J Chem Phys. 2011 Dec 28;135(24):245104. doi: 10.1063/1.3670877.

PMID:
22225189
17.

[Relationship between the molecular structure of aqueous solutions of polyethylene glycol and the compactness of double-stranded DNA molecules].

Salianov VI, Pogrebniak VG, Skuridin SG, Lortkipanidze GB, Chidzhavadze ZG.

Mol Biol (Mosk). 1978 May-Jun;12(3):485-95. Russian.

PMID:
661817
18.

1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium.

Chiu TK, Dickerson RE.

J Mol Biol. 2000 Aug 25;301(4):915-45. Erratum in: J Mol Biol 2000 Oct 13;303(1):111.

PMID:
10966796
19.

Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules.

Sinha SK, Bandyopadhyay S.

J Chem Phys. 2011 Mar 21;134(11):115101. doi: 10.1063/1.3560442.

PMID:
21428665

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