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

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 ∝ Lß. At longer lengths, the exponent ß needs to satisfy the condition ß > 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.

Thermal Conductivity of B-DNA.

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 1D 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 conductivities 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 the non-equilibrium approach. In addition, the denaturation regime of B-DNA is obtained from the variation of thermal conductivity with temperature. It is in agreement with previous studies using the Peyrard-Bishop-Dauxois model at a temperature of around 350 K. The quantum heat capacity (Cvq) has given additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA.

Transient dynamic distributed strain sensing using photonic crystal waveguides.

This paper presents a new type of one-dimensional photonic crystal (PC) waveguide sensor and a technique for prediction of transient strain response accurately. The PC waveguide is integrated on a silicon substrate. We investigate the effect of non-uniform strain localization on the optical signal and use that information to capture the transient strain. Wavelength shift due to distributed strain field is modeled by incorporating the mechanically deformed geometry and photo-acoustic coupling through Pockels effect in a finite element formulation. We demonstrate the advantages of using our proposed method, where multiple spectral peak shift is used instead of single peak shift in order to improve sensing output accuracy and also to estimate the sensor parameter regressively, where the signal's bandwidth is limited. The maximum sensitivity of the waveguide sensor in terms of wavelength shift is estimated to be 0.36 pm/µstrain in single-peak-based sensing, whereas the proposed adaptive multispectral estimation scheme shows an enhanced sensitivity of 4.029 pm/µstrain.