Prediction of thermal expansion properties of carbon nanotubes using molecular dynamics simulations

The axial coefficients of thermal expansion (CTE) of various carbon nanotubes (CNTs), i.e., single-wall carbon nanotubes (SWCNTs), and some multi-wall carbon nanotubes (MWCNTs), were predicted using molecular dynamics (MDs) simulations. The effects of two parameters, i.e., temperature and the CNT diameter, on CTE were investigated extensively. For all SWCNTs and MWCNTs, the obtained results clearly revealed that within a wide low temperature range, their axial CTEs are negative. As the diameter of CNTs decreases, this temperature range for negative axial CTEs becomes narrow, and positive axial CTEs appear in high temperature range. It was found that the axial CTEs vary nonlinearly with the temperature, however, they decrease linearly as the CNT diameter increases. Moreover, within a wide temperature range, a set of empirical formulations was proposed for evaluating the axial CTEs of armchair and zigzag SWCNTs using the above two parameters. Finally, it was found that the absolute value of the negative axial CTE of any MWCNT is much smaller than those of its constituent SWCNTs, and the average value of the CTEs of its constituent SWCNTs. The present fundamental study is very important for understanding the thermal behaviors of CNTs in such as nanocomposite temperature sensors, or nanoelectronics devices using CNTs.

Formation of carbon nanoscrolls from graphene nanoribbons : a molecular dynamics study

Carbon nanoscrolls (CNSs) are one of the carbon-based nanomaterials similar to carbon nanotubes (CNTs) but are not widely studied in spite of their great potential applications. Their practical applications are hindered by the challenging fabrication of the CNSs. A physical approach has been proposed recently to fabricate the CNS by rolling up a monolayer graphene nanoribbon (GNR) around a CNT driven by the interaction energy between them. In this study, we perform extensive molecular dynamics (MD) simulations to investigate the various factors that impact the formation of the CNS from GNR. Our simulation results show that the formation of the CNS is sensitive to the length of the CNT and temperature. When the GNR is functionalized with hydrogen, the formation of the CNS is determined by the density and distribution of the hydrogen atoms. Graphyne, the allotrope of graphene, is inferior to graphene in the formation of the CNS due to the weaker bonds and the associated smaller atom density. The mechanism behind the rolling of GNR into CNS lies in the balance between the GNR–CNT van der Waals (vdW) interactions and the strain energy of GNR. The present work reveals new important insights and provides useful guidelines for the fabrication of the CNS.

Thermal behavior of kaolinite–urea intercalation complex and molecular dynamics simulation for urea molecule orientation

The thermal behavior of kaolinite–urea intercalation complex was investigated by thermogravimetry–differential scanning calorimetry (TG–DSC), X-ray diffraction (XRD), and fourier transform infrared spectroscopy (FTIR). In addition, the interaction mode of urea molecules intercalated into the kaolinite gallery was studied by means of molecular dynamics simulation. Three main mass losses were observed at 136 °C, in the range of 210–270 °C, and at 500 °C in the TG–DSC curves, which were, respectively, attributed to (1) melting of the surface-adsorbed urea, (2) removal of the intercalated urea, and (3) dehydroxylation of the deintercalated kaolinite. The three DSC endothermic peaks at 218, 250, and 261 °C were related to the successive removals of intercalated urea with three different distribution structures. Based on the angle between the dipole moment vector of urea and the basal surface of kaolinite, the three urea models could be described as follows: (1) Type A, the dipole moment vector is nearly parallel to the basal surface of kaolinite; (2) Type B, the dipole moment vector points to the silica tetrahedron with the angle between it and the basal surface of kaolinite ranging from 20°to 40°; and (3) Type C, the dipole moment vector is nearly perpendicular to the basal surface of kaolinite. The three distribution structures of urea molecules were validated by the results of the molecular dynamics simulation. Furthermore, the thermal behavior of the kaolinite–urea intercalation complex investigated by TG–DSC was also supported by FTIR and XRD analyses.

Fractal and complex network analyses of protein molecular dynamics

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q)h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2)h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H≈0.5H≈0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2)h(2) of MF-DFA on the time series, exponent λλ of the exponential degree distribution and fractal dimension dBdB of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between 〈h(2)〉〈h(2)〉 (from MF-DFA on time series) and 〈dB〉〈dB〉 of the converted HVGs for different energy, pressure and volume.

Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

The monosaccharide 2-O-sulfo-α-l-iduronic acid (IdoA2S) is one of the major components of glycosaminoglycans. The ability of molecular mechanics force fields to reproduce ring-puckering conformational equilibrium is important for the successful prediction of the free energies of interaction of these carbohydrates with proteins. Here we report unconstrained molecular dynamics simulations of IdoA2S monosaccharide that were carried out to investigate the ability of commonly used force fields to reproduce its ring conformational flexibility in aqueous solution. In particular, the distribution of ring conformer populations of IdoA2S was determined. The GROMOS96 force field with the SPC/E water potential can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution. On the other hand, the GLYCAM06 force field with the TIP3P water potential sampled transitional conformations between the boat and chair forms. Simulations using the GROMOS96 force field showed no pseudorotational equilibrium fluctuations and hence no inter-conversion between the boat and twist boat ring conformers. Calculations of theoretical proton NMR coupling constants showed that the GROMOS96 force field can predict the skew-boat to chair conformational ratio in good agreement with the experiment, whereas GLYCAM06 shows worse agreement. The omega rotamer distribution about the C5–C6 bond was predicted by both force fields to have torsions around 10°, 190°, and 360°.

Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

CXCL-8 (Interleukin 8) is a CXC chemokine with a central role in the human immune response. We have undertaken extensive in silico analyses to elucidate the interactions of CXCL-8 with its various binding partners, which are crucial for its biological function. Sequence and structure analyses showed that residues in the thirdq β-sheet and basic residues in the heparin binding site are highly variable, while residues in the second β-sheet are highly conserved. Molecular dynamics simulations in aqueous solution of dimeric CXCL-8 have been performed with starting geometries from both X-ray and NMR structures showed shearing movements between the two antiparallel C-terminal helices. Dynamic conservation analyses of these simulations agreed with experimental data indicating that structural differences between the two structures at quaternary level arise from changes in the secondary structure of the N-terminal loop, the 310-helix, the 30s, 40s, and 50s loops and the third β-sheet, resulting in a different interhelical separation. Nevertheless, the observation of these different states indicates that CXCL-8 has the potential to undergo conformational changes, and it seems likely that this feature is relevant to the mode of binding of glycosaminoglycan (GAG) mimetics such as cyclitols. Simulations of the receptor peptide fragment−CXCL-8 complex identified several specific interactions of the receptor peptide with CXCL-8 that could be exploited in the structure-based design of competitive peptides and nonpeptidic molecules targeting CXCL-8 for combating inflammatory diseases. Simulations of the CXCL-8 dimer complexed with a 24-mer heparin fragment and of the CXCL-8−receptor peptide complex revealed that Arg60, Lys64, and Arg68 in the dimer bind to cyclitols in a horseshoe pattern, defining a region which is spatially distinct from the receptor binding site. There appears to be an optimum number of sulfates and an optimum length of alkyl spacers required for the interaction of cyclitol inhibitors with the dimeric form of CXCL-8. Calculation of the binding affinities of cyclitol inhibitors reflected satisfactorily the ranking of experimentally determined inhibitory potencies. The findings of these molecular modeling studies will help in the search for inhibitors which can modulate various CXCL-8 biological activities and serve as an excellent model system to study CXC-inhibitor interactions.

Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment

Aggregation of the microtubule associated protein tau (MAPT) within neurons of the brain is the leading cause of tauopathies such as Alzheimer's disease. MAPT is a phospho-protein that is selectively phosphorylated by a number of kinases in vivo to perform its biological function. However, it may become pathogenically hyperphosphorylated, causing aggregation into paired helical filaments and neurofibrillary tangles. The phosphorylation induced conformational change on a peptide of MAPT (htau225−250) was investigated by performing molecular dynamics simulations with different phosphorylation patterns of the peptide (pThr231 and/or pSer235) in different simulation conditions to determine the effect of ionic strength and phosphate charge. All phosphorylation patterns were found to disrupt a nascent terminal β-sheet pattern (226VAVVR230 and 244QTAPVP249), replacing it with a range of structures. The double pThr231/pSer235 phosphorylation pattern at experimental ionic strength resulted in the best agreement with NMR structural characterization, with the observation of a transient α-helix (239AKSRLQT245). PPII helical conformations were only found sporadically throughout the simulations. Proteins 2014; 82:1907–1923. © 2014 Wiley Periodicals, Inc.

Molecular investigation of the mechanical properties of single actin filaments based on vibration analyses

The mechanical vibration properties of single actin filaments from 50 to 288 nm are investigated by the molecular dynamics simulation in this study. The natural frequencies obtained from the molecular simulations agree with those obtained from the analytical solution of the equivalent Euler–Bernoulli beam model. Through the convergence study of the mechanical properties with respect to the filament length, it was found that the Euler–Bernoulli beam model can only be reliably used when the single actin filament is of the order of hundreds of nanometre scale. This molecular investigation not only provides the evidence for the use of the continuum beam model in characterising the mechanical properties of single actin filaments, but also clarifies the criteria for the effective use of the Euler–Bernoulli beam model.

Dynamics deflection analysis of nanoelectromechanical switches based on carbon nanotubes

This paper aims to develop an effective numerical simulation technique for the dynamic deflection analysis of nanotubes-based nanoswitches. The nanoswitch is simplified to a continuum structure, and some key material parameters are extracted from typical molecular dynamics (MD). An advanced local meshless formulation is applied to obtain the discretized dynamic equations for the numerical solution. The developed numerical technique is firstly validated by the static deflection analyses of nanoswitches, and then, the fundamental dynamic properties of nanoswitches are analyzed. A parametric comparison with the results in the literature and from experiments shows that the developed modelling approach is accurate, efficient and effective.

Surface effects on the dual-mode vibration of <110> silver nanowires with different cross-sections

Dual-mode vibration of nanowires has been reported experimentally through actuation of the nanowire at its resonance frequency, which is expected to open up a variety of new modalities for the NEMS that could operate in the nonlinear regime. In the present work, we utilize large scale molecular dynamics simulations to investigate the dual-mode vibration of <110> Ag nanowires with triangular, rhombic and truncated rhombic cross-sections. By incorporating the generalized Young-Laplace equation into Euler-Bernoulli beam theory, the influence of surface effects on the dual-mode vibration is studied. Due to the different lattice spacing in principal axes of inertia of the {110} atomic layers, the NW is also modeled as a discrete system to reveal the influence from such specific atomic arrangement. It is found that the <110> Ag NW will under a dual-mode vibration if the actuation direction is deviated from the two principal axes of inertia. The predictions of the two first mode natural frequencies by the classical beam model appear underestimated comparing with the MD results, which are found to be enhanced by the discrete model. Particularly, the predictions by the beam theory with the contribution of surface effects are uniformly larger than the classical beam model, which exhibit better agreement with MD results for larger cross-sectional size. However, for ultrathin NWs, current consideration of surface effects is still experiencing certain inaccuracy. In all, for all different cross-sections, the inclusion of surface effects is found to reduce the difference between the two first mode natural frequencies. This trend is observed consistent with MD results. This study provides a first comprehensive investigation on the dual-mode vibration of <110> oriented Ag NWs, which is supposed to benefit the applications of NWs that acting as a resonating beam.

A study of vibration and vibration control of ship structures

This paper examines the vibration characteristics and vibration control of complex ship structures. It is shown that input mobilities of a ship structure at engine supports, due to out-of-plane force or bending moment excitations, are governed by the flexural stiffness of the engine supports. The frequency averaged input mobilities of the ship structure, due to such excitations, can be represented by those of the corresponding infinite beam. The torsional moment input mobility at the engine support can be estimated from the torsional response of the engine bed section under direct excitation. It is found that the inclusion of ship hull and deck plates in the ship structure model has little effect on the frequency-averaged response of the ship structure. This study also shows that vibration propagation in complex ship structures at low frequencies can be attenuated by imposing irregularities to the ring frame locations in ships. Vibration responses of ship structures due to machinery excitations at higher frequencies can be controlled by structural modifications of the local supporting structures such as engine beds in ships.

Dynamic matrix control on wind-induced vibration of spatial latticed structures [Chinese title = 空间网壳结构风振抑制的动态矩阵预测控制分析]

Ameliorated strategies were put forward to improve the model predictive control in reducing the wind induced vibration of spatial latticed structures. The dynamic matrix control (DMC) predictive method was used and the reference trajectory which is called the decaying functions was suggested for the analysis of spatial latticed structure (SLS) under wind loads. The wind-induced vibration control model of SLS with improved DMC model predictive control was illustrated, then the different feedback strategies were investigated and a typical SLS was taken as example to investigate the reduction of wind-induced vibration. In addition, the robustness and reliability of DMC strategy were discussed by varying the model configurations.

Semi-active control for structural vibration based on predictive algorithm [Chinese title = 基于预测算法的结构振动半主动控制]

Based on Newmark-β method, a structural vibration response is predicted. Through finding the appropriate control force parameters within certain ranges to optimize the objective function, the predictive control of the structural vibration is achieved. At the same time, the numerical simulation analysis of a two-storey frame structure with magneto-rheological (MR) dampers under earthquake records is carried out, and the parameter influence on structural vibration reduction is discussed. The results demonstrate that the semi-active control based on Newmark-β predictive algorithm is better than the classical control strategy based on full-state feedback control and has remarkable advantages of structural vibration reduction and control robustness.

Reducing MRI gradient coil vibration with rib stiffeners

This work investigates the effect of rib stiffeners on the free and forced vibration of a gradient coil in a Magnetic Resonance Imaging (MRI) scanner. Several reinforcement schemes are studied in this paper. One scheme utilizes the existing holes in the gradient coil structure (typically reserved for magnetic shims) to produce the reinforcement. Non-ferrous, non-magnetic carbon fibre rib stiffeners are employed to fill these holes in several ways to strengthen a gradient coil. Another scheme replaces the inner half of the gradient coil material with a grid of interconnected axial and circumferential rib stiffeners. It is found that the structural stiffness of the gradient coil increases substantially when the coil is reinforced by carbon fibre rib stiffeners. The reinforcement affects the noise and vibration response of the gradient coil structure in the following ways. It increases the frequency range of forced response of the gradient coil at low frequencies due to the increased resonant frequency of the fundamental mode of the coil. Secondly, it reduces the forced response amplitude of the coil structure (which is governed by the structural stiffness of the coil). Thirdly, it reduces the number of natural modes in the low and medium frequency range and therefore lessens the chance of the coil structure being excited resonantly by magnetic resonance signal acquisition sequences. It is shown that gradient coils modelled by solid finite element models have higher stiffness along the coil’s circumference and lower stiffness in the axial direction than those using shell finite element models.