Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Classical Electrostatics for Biomolecular Simulations

(2013) G. Andrés Cisneros et al.   CHEMICAL REVIEWS

The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

(2012) Ivana Beššeová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

(2012) Jejoong Yoo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

(2012) Mahmoud Moradi et al.   NUCLEIC ACIDS RESEARCH

Frontiers in Molecular Dynamics Simulations of DNA

(2011) Alberto Pérez et al.   ACCOUNTS OF CHEMICAL RESEARCH

A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution

(2011) Johan Mähler et al.   INORGANIC CHEMISTRY

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

(2011) Tatsuya Maehigashi et al.   NUCLEIC ACIDS RESEARCH

Electrostatics of Strongly Charged Biological Polymers: Ion-Mediated Interactions and Self-Organization in Nucleic Acids and Proteins

(2010) Gerard C.L. Wong et al.   Annual Review of Physical Chemistry

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

Computational Exploration of Mobile Ion Distributions around RNA Duplex

(2010) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comparative Enzymology and Structural Biology of RNA Self-Cleavage

(2009) Martha J. Fedor   Annual Review of Biophysics

Dependence of A-RNA simulations on the choice of the force field and salt strength

(2009) Ivana Beššeová et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Physical Chemistry of DNA Viruses

(2008) Charles M. Knobler et al.   Annual Review of Physical Chemistry

A repulsive field: advances in the electrostatics of the ion atmosphere

(2008) Vincent B Chu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Molecular dynamics simulations of nucleic acid–protein complexes

(2008) Alexander D MacKerell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin

(2007) Angel E. Garcia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY