Search Results - "Akhshi, Parisa"

Martini Coarse-Grained Force Field: Extension to DNA by Uusitalo, Jaakko J, Ingólfsson, Helgi I, Akhshi, Parisa, Tieleman, D. Peter, Marrink, Siewert J

“…We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to…”
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Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel by Akhshi, Parisa, Mosey, Nicholas J., Wu, Gang

“…How easily can ions move in DNA channels? Three‐dimensional free‐energy landscapes for the movement of Na+, K+, and NH4+ ions through G‐quadruplex DNA channels…”
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Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels by Akhshi, Parisa, Wu, Gang

“…We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion…”
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Fatty Acid Interactions with RNA Building Blocks: Origin of Life Implications by Akhshi, Parisa, Tieleman, Peter

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Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G3T4G4)]2 G‑Quadruplex DNA Structure by Akhshi, Parisa, Acton, Gregory, Wu, Gang

“…We have used both adaptive biasing force (ABF) and regular molecular dynamics (MD) simulations to investigate the asymmetrical NH4 + ion movement inside of a…”
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Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G sub(3)T sub(4)G sub(4))] sub(2) G-Quadruplex DNA Structure by Akhshi, Parisa, Acton, Gregory, Wu, Gang

“…We have used both adaptive biasing force (ABF) and regular molecular dynamics (MD) simulations to investigate the asymmetrical NH sub(4) super(+) ion movement…”
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Development of Coarse-Grained Martini Model for Nucleic Acid Structures by Akhshi, Parisa, Uusitalo, Jaakko, Ingolfsson, Helgi, Marrink, Siewert-Jan, Tieleman, D. Peter

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Coarse-Grained Modeling of DNA-Vesicle Systems with the Martini Force Field by Uusitalo, Jaakko, Ingólfsson, Helgi I., Akhshi, Parisa, Tieleman, D. Peter, Poolman, Bert, Herrmann, Andreas, Marrink, Siewert J.

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Molecular dynamics simulation studies of ion transport along G-quadruplex DNA channels by Akhshi, Parisa

“…Guanine-rich DNA and RNA sequences can fold, in the presence of alkali metal ions such as Na+ and K+, into G-quadruplex structures. These alkali metal ions are…”
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Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel by Akhshi, Parisa, Mosey, Nicholas J., Wu, Gang

“…Wie leicht bewegen sich Ionen durch DNA‐Kanäle? Freie‐Energie‐Hyperflächen für die Bewegung von Na+‐, K+‐ und NH4+‐Ionen durch Kanäle von G‐Quadruplex‐DNA…”
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Free‐Energy Landscapes of Ion Movement through a G‐Quadruplex DNA Channel by Akhshi, Parisa, Mosey, Nicholas J., Wu, Gang

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