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Journal of Biomolecular Structure and Dynamics Volume 31, 2013 - Issue 11
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Articles

Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations

Timothy J. RobbinsDepartment of Chemistry, University of Memphis, Memphis, TN, 38152, USA.
&
Yongmei WangDepartment of Chemistry, University of Memphis, Memphis, TN, 38152, USA.Correspondence[email protected]
Pages 1311-1323 | Published online: 16 Nov 2012

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Timothy J. Robbins & Yongmei Wang. (2013) 88 Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamic simulation and Poisson–Boltzmann approach. Journal of Biomolecular Structure and Dynamics 31:sup1, pages 56-57.
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Articles from other publishers (8)

Makenzie Provorse Long, Serra Alland, Madison E. Martin & Christine M. Isborn. (2020) Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects. Physical Chemistry Chemical Physics 22:10, pages 5584-5596.
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Hong Zhang, Haohao Fu, Xueguang Shao, François Dehez, Christophe Chipot & Wensheng Cai. (2019) Changes in Microenvironment Modulate the B- to A-DNA Transition. Journal of Chemical Information and Modeling 59:5, pages 2324-2330.
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Soham Sarkar, Atanu Maity, Aditya Sarma Phukon, Soumadwip Ghosh & Rajarshi Chakrabarti. (2018) Salt Induced Structural Collapse, Swelling, and Signature of Aggregation of Two ssDNA Strands: Insights from Molecular Dynamics Simulation. The Journal of Physical Chemistry B 123:1, pages 47-56.
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Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski & Joanna Trylska. (2018) Interactions of 2’-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site. PLOS ONE 13:1, pages e0191138.
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Zhong-Liang Zhang, Yuan-Yan Wu, Kun Xi, Jian-Ping Sang & Zhi-Jie Tan. (2017) Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex. Biophysical Journal 113:3, pages 517-528.
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Pablo de Vera, Nigel J. Mason, Fred J. Currell & Andrey V. Solov’yov. (2016) Molecular dynamics study of accelerated ion-induced shock waves in biological media. The European Physical Journal D 70:9.
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Soumadwip Ghosh, Himanshu Dixit & Rajarshi Chakrabarti. (2015) Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach. Chemical Physics 459, pages 137-147.
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Timothy J. Robbins, Jesse D. Ziebarth & Yongmei Wang. (2014) Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson‐Boltzmann approach. Biopolymers 101:8, pages 834-848.
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