Molecular simulation of thermal conductivity in DNA and phonon dispersion in layered materials

Abstract

Heat conduction plays a key role and is linked to the underneath lattice structure. The heat transfer in soft matter materials like DNA and polymers is seldom understood and is deeply linked to the geometry and functional groups in the molecule. Also, probing thermal conduction in shorter length scales using computations gives us a fundamental understanding of the link between structure and phenomena with respect to heat transfer. DNA satisfies the low thermal conductivity requirements for building molecular thermoelectric devices. This was a motivation for this study. Using this motivation, this thesis investigates the thermal conductivity of B-DNA and other layered materials. The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical Molecular Dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1-dimensional model or a coarse-grained model of DNA to reduce simulation times, full atomistic simulations are employed to understand the thermal conduction in B-DNA. Thermal conductivity at different temperatures from 100 to 400 K are investigated using the Einstein-Green-Kubo equilibrium and Müller-Plathe non-equilibrium formalisms. The thermal conductivity of B-DNA at room temperature is found to be 1.5 W/m·K in equilibrium and 1.225 W/m·K in non-equilibrium approach. In addition, the denaturation regime of B-DNA is obtained from the variation of thermal conductivity with temperature. It agrees with previous works using Peyrard-Bishop-Dauxois (PBD) model at a temperature of around 350 K. The quantum heat capacity (Cvq ) has given the additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA. Also, the effect of changing base-pairs on the thermal conductivity of dsDNA, needed investigation at a molecular level. Hence, four sequences, viz. poly(A), poly(G), poly(CG) and poly(AT) were initially analysed in this work. Firstly, length of these sequences was varied from 4-40 base-pairs (bp) at 300 K and the respective thermal conductivity (κ) was computed. Secondly, the temperature dependent thermal conductivities between 100 K and 400 K were obtained in 50 K steps at 28 bp length. The Müller-Plathe reverse non-equilibrium molecular dynamics (RNEMD) was employed to set a thermal gradient and obtain all thermal conductivities in this work. Moreover, mixed sequences using AT and CG sequences, namely A(CG)nT (n=3-7), ACGC(AT)mGCGT (m=0-5) and ACGC(AT)nAGCGT (n=1-4) were investigated based on the hypothesis that these sequences could be better thermoelectrics. 1-dimensional lattices are said to have diverging thermal conductivities at longer lengths, which violate Fourier law. These follow power law, where κ ∝ Lβ . At longer lengths, the exponent β need to satisfythe condition β > 1/3 for divergent thermal conductivity. We find no such significant Fourier law violation through divergence of thermal conductivities at 80 bp lengths or 40 bp lengths.

Also, in the case of second study, the presence of short (m ≤ 2) encapsulated AT sequences within CG sequences show an increasing has given the additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA. Also, the effect of changing base-pairs on the thermal conductivity of dsDNA, needed investigation at a molecular level. Hence, four sequences, viz. poly(A), poly(G), poly(CG) and poly(AT) were initially analysed in this work. Firstly, length of these sequences was varied from 4-40 base-pairs (bp) at 300 K and the respective thermal conductivity (κ) was computed. Secondly, the temperature dependent thermal conductivities between 100 K and 400 K were obtained in 50 K steps at 28 bp length. The Müller-Plathe reverse non-equilibrium molecular dynamics (RNEMD) was employed to set a thermal gradient and obtain all thermal conductivities in this work. Moreover, mixed sequences using AT and CG sequences, namely A ( CG ) n T (n=3-7), ACGC ( AT ) m GCGT (m=0-5) and ACGC ( AT ) n AGCGT (n=1-4) were investigated based on the hypothesis that these sequences could be better thermoelectrics. 1-dimensional lattices are said to have diverging thermal conductivities at longer lengths, which violate Fourier law. These follow power law, where κ ∝ Lβ . At longer lengths, the exponent β need to satisfy the condition β > 13 for divergent thermal conductivity. We find no such significant Fourier law violation through divergence of thermal conductivities at 80 bp lengths or 40 bp lengths. Also, in the case of second study, the presence of short (m ≤ 2) encapsulated AT sequences within CG sequences show an increasing trend. These results are important for engineering DNA based thermal devices. DNA and layered materials are characterized by a stacking periodicity. Whilst in DNA, we have weakly interacting base pair stacking, in layered materials we have Van der Waals interactions . Anharmonicity is strong in both materials. The phonon dispersion of an atomic layer of h-BN and the heat capacity of MAX phase Ti3SiC2 nanolaminates are calculated using ground state density functional theory (DFT) calculations. trend. These results are important for engineering DNA based thermal devices. DNA and layered materials are characterized by a stacking periodicity. Whilst in DNA, we have weakly interacting base pair stacking, in layered materials we have Van der Waals interactions . Anharmonicity is strong in both materials. The phonon dispersion of an atomic layer of h-BN and the heat capacity of MAX phase Ti3SiC2 nanolaminates are calculated using ground state density functional theory (DFT) calculations.