Tatiana Zolotoukhina

Molecular Dynamics Simulation of Heat Transport in a Nanoribbon by the Thermal Wave at Different Durations of Pulse Heating

In recent year, progress has been made in the study of ballistic heat flow and phonon scattering by phonon spectroscopy and phonon-imaging techniques. Regarding the femtosecond laser application to nanostructures, phonon generation in nanoscale electronics is the focus of interest in the investigation of the mechanism of thermal wave formation at different heating pulses and conditions for heat flux propagation in nanostructures. We test an atomic model of thermal transport in a nanoribbon after a few picosecond pulse heating that leads to the simultaneous presence of two modes, namely, coherent phonons and diffusion, by molecular dynamics (MD) simulation. Our main goal is to investigate the characteristics of the highest magnitude vibrational motion of wave front atoms at different heating pulses and ascertain their correspondence to a single longitudinal optical phonon. To this end it is shown that in the MD model, the equations of heat flux taken through the boundaries of a corresponding sampling area can resolve coherent phonon motion with high resolution when translational and vibrational modes are evaluated separately. Such a definition of heat flux allows the tracing of formation and dynamics of a single phonon. It is applied for different times of heating of a nanoribbon sample. The mechanism underlying the decay of phonons into diffusion is also probed, and energy conversion over the nanoribbon is evaluated. The relevant size of the area for the temporal and spatial flux resolution of a coherent phonon in the MD model is confirmed.

Thermal Conductivity of Phonon Modes in Graphene Nanoribbon at Localized High Heating

The spectral components of the phonon transport in the locally thermally excited graphene samples were studied by molecular dynamics (MD) method. In order to be able to select and analyze separate phonon modes in the time of propagation, the transient Green-Kubo approach to the definitions of density of states (DOS) and thermal conductivity was tested in quasi-equilibrium regimes for limited region of the graphene sample studied. Propagation of single modes at the background of diffusional phonon distribution and energy decay of such modes are studied by calculation of the DOS and dispersion relations, their dependence on the heating condition and temperature is studied. Similar conditions can be generated at localized heating of small areas of graphene structures in electronic devices. In transient regime, many issues of thermal transport evaluation still remain not sufficiently tested, especially phonon dynamics. Thermal conductivity of graphene samples related to transport of separate phonon modes is still not completely investigated, however, recent result give indication on the difference in the contribution of phonon modes. In the study, we consider mostly high temperature transport modes that are generated at the heated spot in order to be able to define their velocities and lifetimes in the limit of transient MD sampling.The single-layer graphene nanoribbon of 150 nm to 40 nm was relaxed and prepared in equilibrium in zigzag and armchair orientations. REBO potential for graphene was utilized. Our calculation has shown that at the heating to high temperatures of 1000K and higher, the G mode of graphene remains stationary and has a minimal contribution into thermal transport by coherent modes. The coherent phonon mode or modes that contribute the most into thermal transport were confined in the vicinity of 30 THz and can possibly be attributed to the D modes of graphene.Copyright

MD Evaluation of the IR Spectra of DNA Bases in the Process of Transport Through Graphene Nanopore

Development of the 1D and 2D IR spectroscopy of small organic molecules and clusters opens yet another way of possible identification of small organic molecules in the state of motion in the graphene nanopore scanning device. With the advantage of obtaining qualitative and at least semi-quantitative information of specimens real-time and non-invasively, vibrational spectroscopy techniques, infrared (IR) and Raman have become more and more important in the analysis of biomolecular samples. At present, the sensitivity and spatial resolution of these techniques stands at the challenge of the detection and analysis of biosamples at very low concentration (single molecule) and high spatial resolution (nanometer/sub-nanometer scale). Spectral analysis requires theoretical assignment of vibrational modes to each biomolecule.We considered vibrational spectra of DNA nucleobase at the time when they are translocated through the graphene nanopore. The Fourier transform of the density of states (DOS) of each base was calculated and the spectra of the base molecules and C atoms of graphene pore edge were obtained. Translocation rate was fixed to have maximum interaction of the base with 1.5 nm pore and single orientation of nucleobases was evaluated relative to molecular plane. Whether interaction of nucleobase and nanopore is able to enhance the signal is still remains unanswered. But we have shown that the spectra of each nucleobase are different and can be considered the fingerprint of the particular molecule.The interaction forces between pore and base are structure dependent and time-limited by translocation time. In such case, transient correlation functions were utilized for the DOSes of the individual bases and forces on each atom of the particular base were sorted by intensity. The spectra of individual atoms in the bases as well as of whole molecule were compared and frequencies of most intense peaks were related to particular atoms. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases can simultaneously give additional information for the electronic transport calculations with possible tra and graphene are of the MM2/MM3 part of the Van der Waals interaction only has been considered. Possibility of base identification by spectral signature is confirmed. Calculated spectra are compared with results of the existing IR measurements for nucleobases.Copyright

Individual DNA Base Identification at the Transport Through Graphene Nanopore

Use of solid film nanopore in which DNA is threaded through for efficient DNA sequencing devices has various practical issues concerned with nucleobase motion that should be controlled. Translocation rate and different orientation of nucleobases, stochastic motion of single-strand DNA through a nanopore introduce definite amount of noise into the signal defining interaction of nucleobase and nanopore. We propose to consider the single layer graphene nanopore as a two-way interaction scanning device.The interaction forces between pore and base are structure dependent, even within orientation and noise average over a base, and can be evaluated. The appropriate translocation rate of the base molecule provide a time-dependent function of interaction change inside of interaction interval of each individual base with graphene nanopore. In such case transient characteristics of the individual bases can be used for identification of the bases. The forces between bases and graphene nanopore of 1.5nm diameter are calculated as interaction characteristics of bases. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases and graphene are of the MM2/MM3 type although the possibility of the Van der Waals interaction only can also be considered. The noise of the force signal due to orientation of the bases in the pore is evaluated and base-dependent interaction recognition is considered relative to the magnitude of the AFM signal in the non-contact mode. The time-dependent in-plane for graphene transient force signal resolution for different bases is probed. Possibility of base identification by combination of transient in-plane force taken as orientation averaged signal is studied. Obtained results can simultaneously give additional information for the electronic transport calculations with possible transient base orientations relative to the edge of pore in graphene.Copyright

Molecular Dynamics Simulation of Coherent Phonon Generation and Its Spectral Characterization in a Nanoribbon upon Localized Pulse Heating

The generation and thermal transport of coherent phonons during instantaneous pulse heating in the presence of diffusion is studied by a molecular dynamics (MD) method. Coherent phonon formation and propagation characteristics are obtained and compared for different shapes of the heating pulse, such as a half-period square, a Gaussian, and a triangle, using the Lennard-Jones (LJ) nanoribbon model. Heating energy exceeding the equilibrium energy distribution of a heated region relaxes by emitting a train of (3 to 5) coherent phonons. As shown in the MD model, the equations of heat flux can resolve coherent phonon motion with high resolution when flux through the boundaries is evaluated with sampling regions of the same size as a single phonon vibration period in the direction of propagation. In the presence of diffusion, the dependence of the generation and decay of phonons on the energy density of the heating pulse is studied for different heating times of the nanoribbon sample. Heating pulses of different duration with a Gaussian profile lead to a higher percentage of heating energy being converted into coherent phonons relative to other pulse shapes. The number of generated phonons and their amplitudes are shown to vary with the pulse duration and shape owing to differences in the energy density of the heating pulses. In the phonon propagation sampling regions, the density of states (DOS) is used to identify coherent phonon frequencies, which are shown to correspond, in terms of the number of identified phonons, to the shape of the thermal envelope for the different pulse shapes and heating times of the nanoribbon sample.

Identification of Nucleobases of Single Stranded DNA by Nanopore Force Resolution at Different Film Thickness

The model of the molecular translocation of all types of DNA base molecules of cytosine, thymine, adenine and guanine through the nanoporous membrane of a solid thin film has been considered from the point of view of improving the resolution of forces by changing parameters of the membrane itself. The results of simulation of translocation process were compared for all four DNA nucleotides. The molecular dynamics (MD) method with the force field potential has been used for the atomic level modeling of the cytosine (C), thymine (T), adenine (A), and guanine (G) molecules and a configuration of the nanoporous Si membrane. With the planar structure of base molecules and cylindrical symmetry of pore, the two-dimensional projection was used in the simulation. The force field between the base molecule and atoms of nanopore has been estimated. Influence of the Si surface hydrogenization and film thickness on the force resolution for each nucleobase was evaluated vs. possible signal resolution. At 5 layer thickness of the film it was possible to cut thermal fluctuations and distinguish four nucleobase types.Copyright