S. Kirmizialtin

Sequence-dependent orientational coupling and electrostatic attraction in cation-mediated DNA-DNA interactions

This study elucidates DNA condensation mechanisms by analyzing cation dynamics and sequence-dependent interactions under different salt conditions.

RNA triplex structures revealed by WAXS-driven MD simulations

This paper uses WAXS-driven MD simulations to reveal RNA triplex structures that are difficult to characterize by crystallography.

Differences in Ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts

The paper uses molecular dynamics simulations to show that Na+ stabilizes RNA more than K+ due to differences in ion-RNA binding modes related to charge density.

Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid

This study investigates the conformational dynamics and kinetics of nucleotide misincorporation and mismatch extension in a high-fidelity DNA polymerase using fluorescent unnatural amino acids and molecular dynamics simulations.

Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis

This study analyzes the roles of two Mg2+ ions in DNA polymerase specificity and catalysis using kinetic analysis and molecular dynamics simulations.

Dramatic shape changes occur as Cytochrome c folds

The paper uses simulations to study Cytochrome c folding, showing dramatic shape changes from an unfolded prolate ellipsoid to a spherical native state through a sequential mechanism.

Structure-guided DNA-DNA attraction mediated by divalent cations

This study identifies sequence-dependent DNA-DNA condensation mediated by divalent cations, revealing a mechanism involving sequence-enhanced major groove binding.