Faculty Publications

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Subject: search.filters.subject.Classical molecular dynamics

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Now showing 1 - 7 of 7
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    Young's modulus of defective graphene sheet from intrinsic thermal vibrations
    (Institute of Physics Publishing helen.craven@iop.org, 2016) Thomas, S.; Mrudul, M.S.; Ajith, A.; Valsakumar, M.C.
    Classical molecular dynamics simulations have been performed to establish a relation between thermally excited ripples and Young's modulus of defective graphene sheet within a range of temperatures. The presence of the out-of-plane intrinsic ripples stabilizes the graphene membranes and the mechanical stability is analyzed by means of thermal mean square vibration amplitude in the long wavelength regime. We observed that the presence of vacancy and Stone-Wales (SW) defects reduces the Young's modulus of graphene sheets. Graphene sheet with vacancy defects possess superior Young's modulus to that of a sheet with Stone-Wales defects. The obtained room temperature Young's modulus of pristine and defective graphene sheet is ∼ 1 TPa, which is comparable to the results of earlier experimental and atomistic simulation studies. © Published under licence by IOP Publishing Ltd.
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    Directional anisotropy, finite size effect and elastic properties of hexagonal boron nitride
    (Institute of Physics Publishing helen.craven@iop.org, 2016) Thomas, S.; Ajith, K.M.; Valsakumar, M.C.
    Classical molecular dynamics simulations have been performed to analyze the elastic and mechanical properties of two-dimensional (2D) hexagonal boron nitride (h-BN) using a Tersoff-type interatomic empirical potential. We present a systematic study of h-BN for various system sizes. Young's modulus and Poisson's ratio are found to be anisotropic for finite sheets whereas they are isotropic for the infinite sheet. Both of them increase with system size in accordance with a power law. It is concluded from the computed values of elastic constants that h-BN sheets, finite or infinite, satisfy Born's criterion for mechanical stability. Due to the the strong in-plane sp2 bonds and the small mass of boron and nitrogen atoms, h-BN possesses high longitudinal and shear velocities. The variation of bending rigidity with system size is calculated using the Foppl-von Karman approach by coupling the in-plane bending and out-of-plane stretching modes of the 2D h-BN. © 2016 IOP Publishing Ltd.
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    Empirical potential influence and effect of temperature on the mechanical properties of pristine and defective hexagonal boron nitride
    (Institute of Physics Publishing helen.craven@iop.org, 2017) Thomas, S.; Ajith, K.M.; Valsakumar, M.C.
    The major objective of this work is to present results of a classical molecular dynamics study to investigate the effect of changing the cut-off distance in the empirical potential on the stress-strain relation and also the temperature dependent Young's modulus of pristine and defective hexagonal boron nitride. As the temperature increases, the computed Young's modulus shows a significant decrease along both the armchair and zigzag directions. The computed Young's modulus shows a trend in keeping with the structural anisotropy of h-BN. The variation of Young's modulus with system size is elucidated. The observed mechanical strength of h-BN is significantly affected by the vacancy and Stone-Wales type defects. The computed room temperature Young's modulus of pristine h-BN is 755 GPa and 769 GPa respectively along the armchair and zigzag directions. The decrease of Young's modulus with increase in temperature has been analyzed and the results show that the system with zigzag edge shows a higher value of Young's modulus in comparison to that with armchair edge. As the temperature increases, the computed stiffness decreases and the system with zigzag edge possesses a higher value of stiffness as compared to the armchair counterpart and this behaviour is consistent with the variation of Young's modulus. The defect analysis shows that presence of vacancy type defects leads to a higher Young's modulus, in the studied range with different percentage of defect concentration, in comparison with Stone-Wales defect. The variations in the peak position of the computed radial distribution function reveals the changes in the structural features of systems with zigzag and armchair edges in the presence of applied stress. © 2017 IOP Publishing Ltd.
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    Effect of ripples on the finite temperature elastic properties of hexagonal boron nitride using strain-fluctuation method
    (Academic Press, 2017) Thomas, S.; Ajith, K.M.; Valsakumar, M.C.
    This work intents to put forth the results of a classical molecular dynamics study to investigate the temperature dependent elastic constants of monolayer hexagonal boron nitride (h-BN) between 100 and 1000 K for the first time using strain fluctuation method. The temperature dependence of out-of-plane fluctuations (ripples) is quantified and is explained using continuum theory of membranes. At low temperatures, negative in-plane thermal expansion is observed and at high temperatures, a transition to positive thermal expansion has been observed due to the presence of thermally excited ripples. The decrease of Young's modulus, bulk modulus, shear modulus and Poisson's ratio with increase in temperature has been analyzed. The thermal rippling in h-BN leads to strong anharmonic behaviour that causes large deviation from the isotropic elasticity. A detailed study shows that the strong thermal rippling in large systems is also responsible for the softening of elastic constants in h-BN. From the determined values of elastic constants and elastic moduli, it has been elucidated that 2D h-BN sheets meet the Born's mechanical stability criterion in the investigated temperature range. The variation of longitudinal and shear velocities with temperature is also calculated from the computed values of elastic constants and elastic moduli. © 2017 Elsevier Ltd
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    Hydrophilicity of the hydrophobic group: Effect of cosolvents and ions
    (Elsevier B.V., 2019) Dilip, H.N.; Chakraborty, D.
    Classical molecular dynamics simulations were performed to study the effect of cosolvents and ions on the solvation structure of zwitterionic glycine in liquid water. Simulations were carried out for 2 M and 1 M concentration of TMAO, Urea, KCl and LiCl solutions to observe the changes in liquid structure of water near the glycine molecule. Radial distribution functions and spatial distribution functions showed the presence of protective hydration layer near the C ? in presence of TMAO which gets reduced in case of urea, KCl and minimum in case of LiCl. LiCl is found to disrupt severely the solvation structure near the glycine molecule. For LiCl system, a small hydration layer is found near C ? unit at higher distances which is mainly due to the first hydration shell of lithium ion bonded to the carboxylate group. Presence of these hydration layers gives extra stabilization energy to the glycine water system. Stabilizing and destabilizing effect of water near the glycine molecule is calculated in terms of Potential Mean Force. The anomalous behaviour of lithium salts with respect to Group I cation salts in protein stabilization can be explained on the basis of this behaviour. We found maximum hydrogen bond lifetime for water molecules in presence of TMAO followed by LiCl, KCl and least in case of urea. The higher lifetimes in presence of ions are found mainly due to their electrostatic force. The stabilization of the hydrophobic part of the glycine molecule can be correlated with the stabilization of proteins in presence of these cosolvents. © 2019 Elsevier B.V.
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    Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides
    (Elsevier B.V., 2020) Dilip, H.N.; Chakraborty, D.
    Effects of two naturally occurring osmolytes, urea and trimethylamine-N-oxide (TMAO) on the solvation structure of hydrophobic moiety of alanine, glycine, N-methylacetamide and acetamide are investigated by classical molecular dynamics simulations. Our results are analysed in terms of site-site radial distribution functions (RDF), spatial distribution functions (SDF), number of hydrogen bonds, orientation profile, KB integrals, preferential binding coefficient and hydrogen bond dynamics. RDF and SDF showed presence of an extra hydration shell near the hydrophobic unit when TMAO is present in the solution. This hydration shell mainly consists of broken hydrogen bonds. In urea-water solution, intramolecular association is favoured compared to intermolecular association: which is in contrast to the TMAO-water solution. Alanine, glycine, NMA and acetamide showed preferred interactions with the water molecules in presence of TMAO compared to urea. Urea and TMAO both are found to be excluded from the alanine, glycine, NMA and acetamide surface but presence of urea was slightly favoured at higher distances in case of NMA and acetamide. The strong hydrogen bond between TMAO-water increases the hydrogen bond lifetime of other hydrogen bonds in the system. The preferential binding affinity of water with the protein molecules and strong hydrogen bonds are found to be the key reasons for stability in presence of TMAO. © 2019 Elsevier B.V.
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    Anharmonicities in the temperature-dependent bending rigidity of BC3 monolayer
    (Elsevier Ltd, 2020) Mrudul, M.S.; Thomas, S.; Ajith, K.M.
    The present work investigated the temperature-dependent thermodynamic and structural characteristics of graphene-like monolayer boron carbide (g-BC3) using classical molecular dynamics simulations. Herein, we mainly focused on the temperature dependence of mean square displacement of thermally stimulated ripples and bending rigidity of g-BC3. We observed that at high temperatures, the specific heat capacity at constant volume exhibits a significant increase beyond the limit of Dulong-Petit value due to the presence of anharmonicity in the g-BC3. Besides, the linear thermal expansion coefficient is found to be negative owing to the excitation of low-frequency bending vibrations in the out-of-plane orientation. Studies reveal that the out-of-plane of height fluctuations and bending rigidity are fully dependent on temperature and are described using the continuum theory of membranes. Moreover, the study on the height fluctuation and correlation shows variation from the estimation of the harmonic theory of membranes as a consequence of the anharmonic features of g-BC3. We believe that our study will provide a notable contribution to numerous applications of g-BC3 including nanoelectromechanical (NEMS) devices to become a reality. © 2020 Elsevier Ltd