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    Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein
    (Iop Publishing Ltd, 2016) Asafi, M. S.; Yildirim, A.; Tekpinar, M.
    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.
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    Öğe
    First-principles study of the structural, elastic, electronic, optical, and vibrational properties of intermetallic Pd 2Ga
    (2012) Yildirim, A.; Koc, H.; Deligoz, E.
    The structural, elastic, electronic, optical, and vibrational properties of the orthorhombic Pd 2Ga compound are investigated using the norm-conserving pseudopotentials within the local density approximation in the frame of density functional theory. The calculated lattice parameters have been compared with the experimental values and found to be in good agreement with these results. The second-order elastic constants and the other relevant quantities, such as the Young's modulus, shear modulus, Poisson's ratio, anisotropy factor, sound velocity, and Debye temperature, have been calculated. It is shown that this compound is mechanically stable after analysing the calculated elastic constants. Furthermore, the real and imaginary parts of the dielectric function and the optical constants, such as the optical dielectric constant and the effective number of electrons per unit cell, are calculated and presented. The phonon dispersion curves are derived using the direct method. The present results demonstrate that this compound is dynamically stable. © 2012 Chinese Physical Society and IOP Publishing Ltd.