Microstructure evolution and plastic deformation of Ni47Co53 alloy under tension

To investigate microstructural evolution and plastic deformation under tension conditions, the rapid solidification processes of Ni47Co53 alloy are first simulated by molecular dynamics methods at cooling rates of 1011, 1012...

Deformation mechanism of copper reinforced by three-dimensional graphene under torsion and tension

The mechanical behaviors of uniaxial torsional and tensional copper nanorod embedded with sp2-type hybrid graphene nanosheets (3DG/Cu) were investigated systematically using molecular dynamics methods. During the torsion process, graphene expanded the plastic deformation region of copper, while the plastic deformation in monocrystalline Cu cases was limited to a smaller area. 3DG/Cu responded to the torsion by one more plastic stage when plastic deformation spread along the length after the elastic response. Graphene improved the torsional loading capacity of the composite material, greatly extending the effective response range of the material by distributing the deformation of copper along with the graphene rather than being concentrated at a certain position like monocrystalline Cu. Generally, as the length of the model increased, this enhancement decreased. The copper portion of 3DG/Cu was divided into three areas during uniaxial tensile, a static region, a quasi-static region of the middle portion where the shear and necking occurred, and a dynamic area near the loading end. However, the inside graphene kept continuous until fracture. Furthermore, graphene improved the yield strain of copper by maintaining intact after copper failure. The greater the pre-loaded torsion angle, the smaller the yield strength and Young's modulus of 3DG/Cu.

Molecular Simulation of the Adsorption Characteristics of Methane in Pores of Coal with Different Metamorphic Degrees

In order to study differences in the methane adsorption characteristics of coal pores of different metamorphic degrees, 4 nm pore structure models based on three typical coal structure models with different metamorphic degrees were constructed. Based on the molecular mechanics and dynamics theory, the adsorption characteristics of methane in different coal rank pores were simulated by the grand canonical Monte Carlo (GCMC) and molecular dynamics methods. The isothermal adsorption curve, Van der Waals energy, concentration distribution, and diffusion coefficient of methane under different conditions were analyzed and calculated. The results showed that at the same pore size, the adsorption capacity of CH4 is positively correlated with pressure and metamorphic degree of coal, and the adsorption capacity of CH4 in high metamorphic coal is more affected by temperature. The relative concentration of CH4 in high-order coal pores is low, and the relative concentration at higher temperature and pressure conditions is high. The CH4 diffusion coefficient in high-rank coal is low, corresponding to the strong Van der Waals interaction between CH4 and coal. The research results are of great significance for further exploration of the interaction mechanism between CH4 and coal with different metamorphic degrees and can provide theoretical support for the selection of gas extraction parameters.

Effect of the THF molecules on the hydrate cavities formation with adding NaCL molecules into the modeling system

In this work, using molecular dynamics methods by Gromacs package we simulate the hydrate formation in systems containing THF, water, and NACL molecules at different thermodynamic conditions and concentration of THF molecules. The curves of the number of hydrogen bonds are obtained depending on the simulation time at different temperatures. The computer simulations results show that the hydrogen bonds between THF and water molecules are relatively weak, with a maximum number of two water molecules hydrogen bonded to THF, but THF can facilitate water molecules rearrangement to form a pentagonal or hexagonal planar ring that is the part of clathrate cavity. In addition, the THF molecule can significantly increase the likelihood to form clathrate cavities suitable for the second guest molecule. The effect of THF molecules concentration on the hydrate cavities formation with adding NaCL molecules into the modeling system is shown. In this work, data are obtained on the magnitude of torsion angles, the percentage of which increases depending on the simulation time, which allows concluding that labile large and small cavities of sII hydrates are formed. The increase in the THF molecules concentration is shown to lead to a decrease in the hydrogen bonds number of water molecules in the simulated system.

Bacterial Luciferases from Vibrio harveyi and Photobacterium leiognathi Demonstrate Different Conformational Stability as Detected by Time-Resolved Fluorescence Spectroscopy

Detecting the folding/unfolding pathways of biological macromolecules is one of the urgent problems of molecular biophysics. The unfolding of bacterial luciferase from Vibrio harveyi is well-studied, unlike that of Photobacterium leiognathi, despite the fact that both of them are actively used as a reporter system. The aim of this study was to compare the conformational transitions of these luciferases from two different protein subfamilies during equilibrium unfolding with urea. Intrinsic steady-state and time-resolved fluorescence spectra and circular dichroism spectra were used to determine the stages of the protein unfolding. Molecular dynamics methods were applied to find the differences in the surroundings of tryptophans in both luciferases. We found that the unfolding pathway is the same for the studied luciferases. However, the results obtained indicate more stable tertiary and secondary structures of P. leiognathi luciferase as compared to enzyme from V. harveyi during the last stage of denaturation, including the unfolding of individual subunits. The distinctions in fluorescence of the two proteins are associated with differences in the structure of the C-terminal domain of α-subunits, which causes different quenching of tryptophan emissions. The time-resolved fluorescence technique proved to be a more effective method for studying protein unfolding than steady-state methods.

Encapsulation of Rhodamine 6G Dye Molecules for Affecting Symmetry of Supramolecular Crystals of Melamine-Barbiturate

Supramolecular organic systems can be used as a host for the encapsulation of small organic molecules. Here, we chose melamine barbiturate as a robust system capable of supramolecular assembly and the Rhodamine 6G dye entrapment as a guest molecule. The encapsulation of the dye was investigated by UV-visible spectroscopy, SEM and optical fluorescent microscopy while the insight into the crystal structure of the system was obtained by single crystal and powder XRD. For investigation of the system’s properties on a molecular level, the DFT and Classical Molecular Dynamics methods were utilized. Surprisingly, both theoretical and experimental data show not only the successful encapsulation of Rhodamine 6G molecules inside the supramolecular assembly, but also that inclusion of such molecules leads to the drastic improvement in the organic crystal shape. The melamine barbiturate in presence of the Rhodamine 6G molecules tend to form crystals with lesser degree of twinning and higher symmetry in shape than the ones without dye molecules.

Evaluation of Mixed Quantum-Classical Molecular Dynamics on cis‐Azobenzene Photoisomerization

The quantitative prediction on nonadiabatic transitions between different electronic state is important to understand ultrafast processes in photochemistry. A variety of mixed quantum-classical molecular dynamics methods such as surface hopping...