Predicting Phonon Transport in Two-Dimensional Boron Nitride-Graphene Superlattices

2014 ◽  
Author(s):  
Carlos da Silva ◽  
Julia Sborz ◽  
David A. Romero ◽  
Cristina H. Amon
Keyword(s):  
Boron Nitride ◽  
Normal Mode Analysis ◽  
Phonon Transport ◽  
Mode Analysis ◽  
Spectral Energy ◽  
Phonon Modes ◽  
Support Engineering ◽  
Group Velocities ◽  
Phonon Properties

The synthesis of boron nitride (BN) - graphene hybrid materials is now a reality that has opened opportunities for creation of new nanostructures with enhanced mechanical, electronic and thermal properties, of particular interest for nanoelectronics applications. Properties of these materials are still not well understood, and modelling approaches are needed to support engineering design of these novel nanostructures. In this work, we study thermal transport in BN-graphene superlattices from a phonon transport perspective. We predict phonon properties (phonon group velocities and phonon lifetimes) using normal mode analysis based on phonon spectral energy density (SED) in these superlattices, with especial emphasis on the role of the orientation of the atoms at the BN - graphene interfaces. We consider various superlattices compositions with two highly symmetric orientation, i.e., zig-zag and armchair. Our results show that phonon group velocities are higher for the zig-zag interface orientation. We also found that phonon modes at small frequencies are more sensitive to the superlattice configurations.

Mode-Wise Phonon Properties of Bismuth Telluride

2012 ◽  
Author(s):  
Yaguo Wang ◽  
Xianfan Xu
Keyword(s):  
Bismuth Telluride ◽  
Thermal Transport ◽  
Phonon Dispersion ◽  
Normal Mode Analysis ◽  
Relaxation Times ◽  
Mode Analysis ◽  
Phonon Modes ◽  
Time Resolved ◽  
Transport Control ◽  
Phonon Properties

Thermal transport properties and thermal transport control are important for many materials, for example, low thermal conductivity is desirable for thermoelectric materials. Knowledge of mode-wise phonon properties is crucial to identify dominant phonon modes for thermal transport and design effective phonon barriers for thermal transport control. In this paper, we adopt the normal mode analysis to investigate spectral phonon properties, and to calculate phonon dispersion relations and phonon relaxation times in bismuth telluride. Our results agree with previously reported data for long-wavelength longitudinal acoustic phonon and A1g optical phonon obtained from ultrafast time-resolved measurements. By combing the frequency dependent anharmonic phonon group velocities and lifetime, mode-wise thermal conductivities are predicted to reveal the contributions of heat carriers with different polarizations and wavelength.

Mode-Resolved Thermal Conductivity of Freestanding and Supported Bismuth Telluride Quintuple Layer

2016 ◽  
Author(s):  
Cheng Shao ◽  
Hua Bao
Keyword(s):  
Heat Transfer ◽  
Thermal Conductivity ◽  
Bismuth Telluride ◽  
Normal Mode Analysis ◽  
Relaxation Times ◽  
Phonon Transport ◽  
Mode Analysis ◽  
Underlying Mechanisms ◽  
Dynamics Simulations ◽  
Phonon Properties

The successful exfoliation of atomically-thin bismuth telluride quintuple layer (QL) attracts tremendous interest in investigating the electron and phonon transport properties in this quasi-two-dimensional material. While experimental results show that thermal conductivity is significantly reduced in Bi2Te3 QL compared to the bulk phase, the underlying mechanisms for the reduction is still unclear. Also in some measurements, the Bi2Te3 QL is usually supported on the substrate and the effect of the substrate on heat transfer in Bi2Te3 QL is unknown. In this work, we have performed molecular dynamics simulations and normal mode analysis to study the mode-wise phonon properties in freestanding and supported Bi2Te3 QL. We found that the existing of substrate will decrease the phonon relaxation times in Bi2Te3 QL in the full frequency range. Thermal conductivity accumulation function for both freestanding and supported Bi2Te3 QL are constructed and compared. We found that half of heat transfer in freestanding Bi2Te3 QL contributed from phonons with mean free paths larger than 16.5 nm, while in supported Bi2Te3 QL this value is reduced to 11 nm. In both cases phonons with MFPs in the range of 10–30 nm are the dominate heat carriers, which contribute to 55% and 53% of thermal conductivity in freestanding and supported cases.

Coupling Between Phonons and Fluid Particles in Water/Carbon Nanotube Systems

2009 ◽  
Author(s):  
A. J. H. McGaughey ◽  
J. A. Thomas ◽  
J. Turney ◽  
R. M. Iutzi
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Relaxation Times ◽  
Mean Free Path ◽  
Phonon Transport ◽  
Dynamics Simulation ◽  
Spectral Energy ◽  
Total Thermal Conductivity ◽  
Phonon Modes

We investigate thermal transport in water/carbon nanotube (CNT) composite systems using molecular dynamics simulations. Carbon-carbon interactions are modeled using the second-generation REBO potential, water-water interactions are modeled using the TIP4P potential, and carbon-water interactions are modeled using a Lennard-Jones potential. The thermal conductivities of empty and water-filled CNTs with diameters between 0.83 nm and 1.66 nm are predicted using molecular dynamics simulation and a direct application of the Fourier law. For empty CNTs, the thermal conductivity decreases with increasing CNT diameter. As the CNT length approaches 1 micron, a length-independent thermal conductivity is obtained, indicative of diffusive phonon transport. When the CNTs are filled with water, the thermal conductivity decreases compared to the empty CNTs and transitions to diffusive phonon transport at shorter lengths. To understand this behavior, we calculate the spectral energy density of the empty and water-filled CNTs and calculate the mode-specific group velocities, relaxation times, and thermal conductivity. For the empty 1.10 nm diameter CNT, we show that the acoustic phonon modes account for 65 percent of the total thermal conductivity. This behavior is attributed to their long mean-free paths. When the CNT is filled with water, interactions with the water molecules shorten the acoustic mode mean-free path and lower the overall CNT thermal conductivity.

THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS

2003 ◽  
Vol 13 (04) ◽  
pp. 903-936 ◽  
Author(s):  
T. GLOBUS ◽  
D. WOOLARD ◽  
M. BYKHOVSKAIA ◽  
B. GELMONT ◽  
L. WERBOS ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Low Frequency ◽  
Biological Materials ◽  
Mode Analysis ◽  
Resonance Structure ◽  
Terahertz Frequency ◽  
Dna Molecules ◽  
Phonon Modes

The terahertz frequency absorption spectra of DNA molecules reflect low-frequency internal helical vibrations involving rigidly bound subgroups that are connected by the weakest bonds, including the hydrogen bonds of the DNA base pairs, and/or non-bonded interactions. Although numerous difficulties make the direct identification of terahertz phonon modes in biological materials very challenging, recent studies have shown that such measurements are both possible and useful. Spectra of different DNA samples reveal a large number of modes and a reasonable level of sequence-specific uniqueness. This chapter utilizes computational methods for normal mode analysis and theoretical spectroscopy to predict the low-frequency vibrational absorption spectra of short artificial DNA and RNA. Here the experimental technique is described in detail, including the procedure for sample preparation. Careful attention was paid to the possibility of interference or etalon effects in the samples, and phenomena were clearly differentiated from the actual phonon modes. The results from Fourier-transform infrared spectroscopy of DNA macromolecules and related biological materials in the terahertz frequency range are presented. In addition, a strong anisotropy of terahertz characteristics is demonstrated. Detailed tests of the ability of normal mode analysis to reproduce RNA vibrational spectra are also conducted. A direct comparison demonstrates a correlation between calculated and experimentally observed spectra of the RNA polymers, thus confirming that the fundamental physical nature of the observed resonance structure is caused by the internal vibration modes in the macromolecules. Application of artificial neural network analysis for recognition and discrimination between different DNA molecules is discussed.

scholarly journals Dynamics-function relationship of N-terminal acetyltransferases: the β6β7 loop modulates substrate accessibility to the catalytic site

2018 ◽  
Author(s):  
Angèle Abboud ◽  
Pierre Bédoucha ◽  
Jan Byška ◽  
Thomas Arnesen ◽  
Nathalie Reuter
Keyword(s):  
Normal Mode Analysis ◽  
Network Models ◽  
Catalytic Site ◽  
Mode Analysis ◽  
Ligand Specificity ◽  
Hairpin Loop ◽  
Domains Of Life ◽  
Function Relationship ◽  
Relationship Of

N-terminal acetyltransferases (NATs) are enzymes catalysing the transfer of the acetyl from Ac-CoA to the N-terminus of proteins, one of the most common protein modifications. Unlike NATs, lysine acetyltransferases (KATs) transfer an acetyl onto the amine group of internal lysines. To date, not much is known on the exclusive substrate specificity of NATs towards protein N-termini. All the NATs and some KATs share a common fold called GNAT. The main difference between NATs and KATs is an extra hairpin loop found only in NATs called β6β7 loop. It covers the active site as a lid. The hypothesized role of the loop is that of a barrier restricting the access to the catalytic site and preventing acetylation of internal lysines. We investigated the dynamics-function relationships of all available structures of NATs covering the three domains of life. Using elastic network models and normal mode analysis, we found a common dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove, formed by the β4 and β5 strands and three relatively more dynamic loops α1α2, β3β4 and β6β7. We identified two independent dynamical domains in the GNAT fold, which is split at the β5 strand. We characterized the β6β7 hairpin loop slow dynamics and show that its movements are able to significantly widen the mouth of the ligand binding site thereby influencing its size and shape. Taken together our results show that NATs may have access to a broader ligand specificity range than anticipated.

scholarly journals First-principles interpretation of electron transport though single-molecule junctions using molecular dynamics of electron attached states

2021 ◽  
Author(s):  
Dávid P. Jelenfi ◽  
Attila Tajti ◽  
Péter G. Szalay
Keyword(s):  
Molecular Dynamics ◽  
Electron Transport ◽  
Single Molecule ◽  
Transition Probabilities ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Bending Vibrations ◽  
Time Resolved ◽  
State Models

The electron transport through the single-molecule junction of 1,4-Diaminobenzene (BDA) is modeled using ab initio quantum-classical molecular dynamics of electron attached states. Observations on the nature of the process are made by time-resolved analysis of energy differences, non-adiabatic transition probabilities and the spatial distribution of the excess electron. The role of molecular vibrations that facilitate the transport by being responsible for the periodic behaviour of these quantities is shown using normal mode analysis. The results support a mechanism involving the electron's direct hopping between the electrodes, without its presence on the molecule, with the prime importance of the bending vibrations that periodically alter the molecule{electrode interactions. No relevant differences are found between results provided by the ADC(2) and SOS-ADC(2) excited state models. Our approach provides an alternative insight into the role of nuclear motions in the electron transport process, one which is more expressive from the chemical perspective.

scholarly journals NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability

2015 ◽  
Vol 112 (41) ◽  
pp. E5575-E5582 ◽  
Author(s):  
Etana Padan ◽  
Tsafi Danieli ◽  
Yael Keren ◽  
Dudu Alkoby ◽  
Gal Masrati ◽  
...  
Keyword(s):  
Ph Regulation ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Evolutionary Analysis ◽  
Significant Activity ◽  
Helical Hairpin ◽  
The Stability ◽  
Regulatory Properties ◽  
Β Sheet

TheEscherichia coliNa+/H+antiporter (Ec-NhaA) is the best-characterized of all pH-regulated Na+/H+exchangers that control cellular Na+and H+homeostasis. Ec-NhaA has 12 helices, 2 of which (VI and VII) are absent from other antiporters that share the Ec-NhaA structural fold. This α-hairpin is located in the dimer interface of the Ec-NhaA homodimer together with a β-sheet. Here we examine computationally and experimentally the role of the α-hairpin in the stability, dimerization, transport, and pH regulation of Ec-NhaA. Evolutionary analysis (ConSurf) indicates that the VI–VII helical hairpin is much less conserved than the remaining transmembrane region. Moreover, normal mode analysis also shows that intact NhaA and a variant, deleted of the α-hairpin, share similar dynamics, suggesting that the structure may be dispensable. Thus, two truncated Ec-NhaA mutants were constructed, one deleted of the α-hairpin and another also lacking the β-sheet. The mutants were studied at physiological pH in the membrane and in detergent micelles. The findings demonstrate that the truncated mutants retain significant activity and regulatory properties but are defective in the assembly/stability of the Ec-NhaA dimer.

Predicting Phonon Properties From Molecular Dynamics Simulations Using the Spectral Energy Density

2011 ◽  
Author(s):  
Joseph E. Turney ◽  
John A. Thomas ◽  
Alan J. H. McGaughey ◽  
Cristina H. Amon
Keyword(s):  
Molecular Dynamics ◽  
Energy Density ◽  
Molecular Dynamics Simulations ◽  
Lattice Dynamics ◽  
Relaxation Times ◽  
Mode Analysis ◽  
Spectral Energy ◽  
Spectral Energy Density ◽  
Dynamics Simulations ◽  
Phonon Properties

Using lattice dynamics theory, we derive the spectral energy density and the relation between the spectral energy density and the phonon frequencies and relaxation times. We then calculate the spectral energy density and phonon frequencies and relaxation times for a test system of Lennard-Jones argon using velocities obtained from molecular dynamics simulations. The phonon properties, which can be used to calculate thermal conductivity, are compared to predictions made using (i) anharmonic lattice dynamics calculations and (ii) a technique that performs normal mode analysis on the positions and velocities obtained from molecular dynamics simulations.

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