Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Subject: search.filters.subject.Molecular Dynamics

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  • Book Part
    Citation - Scopus: 1
    Molecular Dynamics Studies on Nanoscale Gas Transport
    (Springer Science+Business Media, 2015) Beşkök, Ali; Barışık, Murat
    [No abstract available]
  • Conference Object
    Dynamic Recognition of the Nucleosome Core Particle by Select Chromatin Factors
    (Elsevier B.V., 2025) Döseme, H.; Uluçay, T.; Kale, S.
    The intricate interactions between the nucleosome core particle and chromatin-binding proteins control essential biological functions templated by DNA. The nucleosome is a symmetrical and disc-shaped nucleoprotein which binds several chromatin factors in a 2:1 stoichiometry. We report computational evidence for a DNA-sequence-driven emergence of asymmetry whereby the nucleosome binding affinities of the chromatin factors are altered on each side even though the protein factors bind chemically equivalent proteinous interfaces of the nucleosome. Furthermore, none of these proteins interact directly with the nucleosomal DNA. Using atomistic molecular dynamics simulations, we surveyed five chromatin factors that are known to bind the nucleosome in a 2:1 stoichiometry. In four factors, we found that the nucleosomal gyre that binds DNA strongly is also more preferred. These factors are Sir3, PRC1, RCC1, and SAGA-DUB. However, a fifth chromatin factor, 53BP1, prefers the gyre with the weaker DNA binding with higher affinity. We argue that this tunability in nucleosome affinity could be related to the function of the chromatin interactors as 53BP1 could prefer loose DNA gyres to execute its DNA repair function. © 2025 The Authors. Published by Elsevier B.V.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Longitudinal Thermal Conductivity of Cu-Swcnt Core-Shell Nanowire: Molecular Dynamics Simulations
    (Begell House inc, 2023) Toprak, Kasim; Bayazitoglu, Yildiz
    The phonon thermal conductivity of copper core and armchair single-walled carbon nanotube shell (Cu-SWCNT) coaxial nanostructure is presented using the non-equilibrium molecular dynamics (NEMD) simulations method. The study aims to investigate how the ultrathin Cu nanowire affects the thermal conductivity of Cu-SWCNT. The results have revealed that the thermal conductivity of Cu-SWCNT is more than two orders of magnitude higher than that of the Cu core with the contribution of the SWCNT shell. The influences of length, chirality, defect, and core filling on the thermal conductivity of Cu-SWCNT are studied using the two most used C-C potentials, the AIREBO and Tersoff potentials. The bare SWCNT and Cu-SWCNT simulation results revealed that the thermal conductivity using the AIREBO potential is lower than that of Tersoff. Although the thermal conductivity increases with the length of the coaxial tube, it decreases with the chirality and the filling ratio. Increasing the chirality of SWCNT and the Cu core-filling ratio can boost the core copper's contributions to the thermal conductivity, reducing the overall thermal conductivity. The lengths of the thermostat and buffer regions do not significantly affect the thermal conductivity. In addition, the vacancy concentration in heat flow regions effectively reduces thermal conductivity, whereas the vacancy in the thermostat regions does not have a significant effect. The thermal rectification factor defined as changing the imposed heat flux direction is up to 1.73% for the Cu-SWCNT and 2.63% for the SWCNT.
  • Conference Object
    Molecular Modeling of Force Driven Gas Flows in Nano-Channels
    (International Conference on Computational Fluid Dynamics (ICCFD), 2016) Barışık, Murat
    Nano-scale gas transport plays an important role in many micro/nanotechnology applications where the rarefied gas dynamics based solutions are frequently used by maintaining a “dynamic similarity” between low pressure (rarefied) and nano gas flows. However, such a consideration is incomplete since the surface force field effects dominant in nano-levels induce significant variations. In order to specify the surface force effects on gas transport, we define a new parameter (B) as the ratio of force penetration length to the channel height, and studied the length scales and conditions for applicability of current rarefied gas dynamics on nano-scale gas flows. Using Molecular Dynamics, force driven gas flows were characterized as a function of B parameter and Knudsen number. Results showed that for a negligible value of B parameter (B?0) transport can be described by rarefied gas dynamics in the whole Knudsen range while the velocity profiles are parabolic and the variation of mass flow rate shows the well-known Knudsen minimum around Kn=1. As the flow dimension decreases, B becomes a finite value indicating the dominancy of surface force effects over rarefaction, and gas velocities and mass transport significantly deviates from the kinetic theory predictions. © 2016 9th International Conference on Computational Fluid Dynamics, ICCFD 2016 - Proceedings. All rights reserved.