Heat conductivity of DNA double helix

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.Comment: 16 pages, 12 figure

Limiting Phase Trajectories as an Alternative to Nonlinear Normal Modes

AbstractWe discuss a recently developed concept of limiting phase trajectories (LPTs) allowing a unified description of resonance, highly non-stationary processes for a wide range of classical and quantum dynamical systems with constant and varying parameters. This concept provides a far going extension and adequate mathematical description of the well-known linear beating phenomenon to a diverse variety of nonlinear systems ranging from classical multi-particle models to nonlinear quantum tunneling. While stationary (and non-stationary, but non-resonant) oscllations can be described in the framework of non-linear normal modes (NNMs) concept, it is not so in the considered case of resonant non-stationary processes. In the latter case which is characterized by intense energy exchange between different parts of a system, an additiional slow time scale appears. The energy exchange proceeds in this time scale and can be identified as strong modulation of the fast oscillations. The aforementioned resonant non-staionary prcesses include, e.g., targeted energy transfer, non-stationary vibrations of carbon nanotubes, quantum tunneling, auto-resonance and non-conventional synchronization. Besides the non-linear beating, the LPT concept allows one to find the conditions of transition from intense energy exchange to strongly localized (e.g. breather-like) excitations. A special mathematical technique based on the non- smooth temporal transformations leads to the clear and simple description of strongly modulated regimes. The role of LPTs in the theory of resonance non-stationary processes turns out to be similar to that of NNMs in stationary case.As an example we present results of analytical and numerical study of planar dynamics of a string with uniformly distributed discrete masses without a preliminary stretching. Each mass is also affected by grounding support with cubic characteristic (which is equivalent to transversal unstretched string). We consider the most important case of low-energy transversal dynamics. This example is especially instructive because the considered system cannot be linearized. Adequate analytical description of resonance non-stationary processes which correspond to intensive energy exchange between different parts of the system (clusters) in low frequency domain was obtained in terms of LPTs. We have revealed also in these terms the conditions of energy localization on the initially excited cluster. Analytical results are in agreement with the results of numerical simulations. It is shown that the considered system can be used as an efficient energy sink