Heat conductivity of the DNA double helix

Abstract

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains (”beads on a spring”) that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.

Coarse-graining DNA for simulations of DNA nanotechnology

“…The first, which we term the "bottom-up" approach, is to fit the model to results (typically correlation functions) from a finer-grained model, which is usually an empirical all-atom model (e.g. AMBER, CHARMM), [35][36][37]63,64,[67][68][69] although fitting to energies obtained from electronic structure calculations (albeit in the absence of water) 65 has also been performed. The second "topdown" approach is to directly fit the parameters of a physically motivated potential to reproduce measured experimental properties, e.g.…”

Biomechanics of DNA structures visualized by 4D electron microscopy

“…It is also unlikely that the strongly absorbing carbon substrate would rapidly heat the DNA structure and mediate a temperature jump. Using published values for the thermal conductivity (27), specific heat capacity (28), and density (21) of DNA, one can estimate that the DNA membrane, which connects the filaments to the carbon support, heats up on a timescale of about 100 ns after the substrate undergoes a temperature jump, far too slow to explain the oscillations of the filaments that set in promptly after the laser pulse.…”

Heat transport and thermal rectification in molecular junctions: A minimal model approach

“…In particular, within the discussed two-strand ladder, thermal properties of double-or multiple-stranded molecules, such as DNA molecules or α helices in proteins, can be described. [11][12][13] …”

“…[5][6][7][8][9] Due to the structural complexity of such systems, the study of heat transport on a first-principle level becomes difficult, and thus, the development of minimal model approaches provides a very useful starting point. [10][11][12][13][14] In this context, the clarification of issues related to the validity of macroscopic phenomenological laws, e.g., Fourier's law, to describe heat propagation in nanoscale systems has attracted much attention in the field. 15,16 Thus, for harmonic systems, anomalous heat transportdiverging thermal conductivity with increasing system sizeis obtained, and thus, Fourier's law is not valid.…”