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Search results for: NON-EQUILIBRIUM MOLECULAR DYNAMICS

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Search results for: NON-EQUILIBRIUM MOLECULAR DYNAMICS

  • Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics

    Publication

    - ACS Catalysis - Year 2020

    CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...

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  • Molecular Dynamics simulations of thermal conductivity of penta-graphene

    Publication

    The thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...

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  • Influence of addition of carbon nanotubes on rheological properties of selected liquid lubricants - a computer simulation study

    Publication

    - TASK Quarterly - Year 2020

    This work is motivated by the improvement of anti-friction properties of lubricants by addition of CNTs proved experimentally in literature. In particular, a methodology is developed to compute the shear viscosity of liquid lubricants (Propylene Glycol) based on Molecular Dynamics simulation. Non-Equilibrium molecular dynamics (NEMD) approach is used with a reactive force field ReaxFF implemented in LAMMPS. The simulations are...

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  • Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

    Publication
    • P. Weber
    • P. Bełdowski
    • K. Domino
    • D. Ledziński
    • A. Gadomski

    - ENTROPY - Year 2020

    This work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...

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  • Molecular dynamics studies of polyurethane nanocomposite hydrogels

    Publication

    - The European Physical Journal-Special Topics - Year 2013

    Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...

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