Effect of the Base-Pair Sequence on B-DNA Thermal Conductivity

Mahalingam, V and Harursampath, D (2021) Effect of the Base-Pair Sequence on B-DNA Thermal Conductivity. In: Journal of Physical Chemistry B .

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Abstract

The thermal conductivity of double-stranded (ds) B-DNA was systematically investigated using classical molecular dynamics (MD) simulations. The effect of changing the base pair (bp) 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 analyzed in this work. First, the length of these sequences was varied from 4 to 40 bp at 300 K, and the respective thermal conductivity (κ) was computed. Second, the temperature-dependent thermal conductivities between 100 and 400 K were obtained in 50 K steps at 28 bp length. The Müller-Plathe reverse nonequilibrium 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. One-dimensional lattices are said to have diverging thermal conductivities at longer lengths, which violate the Fourier law. These follow the power law, where κ � Lβ. At longer lengths, the exponent β needs to satisfy the 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 the second study, the presence of short (m � 2) encapsulated AT sequences within CG sequences shows an increasing trend. These results are important for engineering DNA-based thermal devices. © 2021 American Chemical Society.

Item Type:	Journal Article
Publication:	Journal of Physical Chemistry B
Publisher:	American Chemical Society
Additional Information:	The copyright for this article belongs to Authors
Keywords:	Bioinformatics; DNA sequences; Molecular dynamics; Thermal conductivity; Thermal Engineering, Base pair sequences; Base pairs; Classical molecular dynamics; Fourier law; Long lengths; Molecular levels; One-dimensional lattice; Reverse nonequilibrium molecular dynamics; Temperature-dependent thermal conductivity; Thermoelectric, DNA
Department/Centre:	Division of Mechanical Sciences > Aerospace Engineering(Formerly Aeronautical Engineering)
Date Deposited:	29 Nov 2021 08:55
Last Modified:	29 Nov 2021 08:55
URI:	http://eprints.iisc.ac.in/id/eprint/70302

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