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Publication Restricted A comparative molecular dynamics study of methylation state specificity of JMJD2A(Koç University, 2009) Ulucan, Özlem; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997Publication Restricted Determination of statistical correlations between methylated lysine residues of histone H3 tail by molecular dynamics simulations(Koç University, 2009) Şanlı, Deniz; Keskin, Özlem; 0000-0002-4202-4049; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 26605Publication Restricted Efficient ranking of metal organic framework adsorbents and membranes using molecular simulations(Koç University, 2017) Sümer, Zeynep; Keskin, Seda; 0000-0001-5968-0336; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 40548Publication Restricted Global optimization of Pt-Cu clusters using a genetic algorithm and density functional theory(Koç University, 2017) Erdem, Ezgi; Erkey, Can; 0000-0001-6539-7748; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 29633Publication Open Access Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses(American Institute of Physics (AIP) Publishing, 1993) Space B.; Rabitz H.; Department of Mathematics; Aşkar, Attila; Faculty Member; Department of Mathematics; College of Sciences; 178822A subspace dynamics method is presented to model long time dynamical events. The method involves determining a set of vectors that span the subspace of the long time dynamics. Specifically, the vectors correspond to real and imaginary low frequency normal modes of the condensed phase system. Most importantly, the normal mode derived vectors are only used to define the subspace of low frequency motions, and the actual time dependent dynamics is fully anhannonic. The resultant projected set of Newton's equations is numerically solved for the subspace motions. Displacements along the coordinates outside the subspace are then constrained during the integration of the equations of motion in the reduced dimensional space. The method is different from traditional constraint methods in that it can systematically deduce and remove both local and collective high frequency motions of the condensed phase system with no a priori assumptions. The technique is well suited to removing large numbers of degrees of freedom, while only keeping the very low frequency global motions. The method is applied to highly anhannonic Lennard-Jones crystal and glass systems. Even in these systems with no intramolecular degrees of freedom or obvious separation of time scales, the subspace dynamics provides a speed up of approximately a factor of 5 over traditional molecular dynamics through use of a larger integration time step. In the cases illustrated here a single set of subspace vectors was adequate over the full time interval, although this is not expected to be true for all systems.Publication Restricted Molecular dynamics simulation study of silicon nanotubes(Koç University, 2008) Yaşar, Mustafa Selçuk; Dereli, Tekin; 0000-0002-6244-6054; Koç University Graduate School of Sciences and Engineering; Physics; 201358Publication Restricted The investigation of RalGDS-Ral signaling pathway via molecular dynamics simulations(Koç University, 2019) Ömür, Meltem Eda; Keskin, Özlem; 0000-0002-4202-4049; Koç University Graduate School of Sciences and Engineering; Molecular Biology and Genetics; 26605