Constant Number Of Atoms Research Articles

A molecular dynamics analysis of the influence of iron corrosion products on the healing process of bitumen

Corrosion of iron materials in the asphalt concrete pavement occurs commonly when the bitumen film peels off, and the generation of corrosion products would affect the healing performance of bitumen. To identify the affection, this research focuses on the influence of iron corrosion products on the healing process of bitumen by molecular dynamics simulation. Firstly, bitumen model and iron corrosion products model were built. Then the healing systems of sandwich structure were constructed, and the simulated temperature were applied to reach equilibrium in the healing process with NVT ensemble (constant number of atoms, volume, and temperature). Dynamic movements of bitumen were characterized by appearance qualitatively. Healing rate of crack and healing rate of bitumen aggregation were held to evaluate the healing effect. Diffusion behaviors, internal force of motivation and interaction effect were also analyzed. The results indicate the duplicity of iron corrosion products in the healing process including the ease for bitumen climbing and the obstruction of bitumen movement. The comprehensive healing index demonstrated that iron corrosion products would reduce the healing degree, which was mainly caused by the obstruction effect and large internal stress generated by severe aggregation of bitumen in the limited space. From the perspective of crack closure and bitumen aggregation degree in the corrosion area, FeO healing systems were healed best, followed by Fe3O4, Fe2O3 and FeOOH. Furthermore, diffusion period of bitumen molecules on the surface of iron corrosion products during the healing process should be regarded as the important period affecting healing.

Molecular Dynamics Simulation to Evaluate the Stability of Tetra-n-butyl Ammonium/Phosphonium Bromide Semiclathrate Hydrates in the Presence and Absence of Methane, Carbon Dioxide, Methanol, and Ethanol Molecules

Stability of tetra-n-butyl ammonium bromide (TBAB) and tetra-n-butyl phosphonium bromide (TBPB) semiclathrate hydrates with a hydration number of 38 is studied by the molecular dynamics (MD) simulation in the absence and presence of methane, carbon dioxide, methanol, and ethanol molecules. All of the simulation runs are performed under NVT (constant number of atoms, volume, and temperature) and NPT (constant number of atoms, pressure, and temperature) conditions using optimized potentials for liquid simulations-all-atom (OPLS-AA) force field with nonpolarizable water models (including SPC, TIP3P, TIP4P, and TIP4P/Ice), where the operating conditions include a temperature range of 250–350 K and pressures of 0.1 and 50 MPa. The potential energy and structural analysis, mean square displacement (MSD), diffusion coefficient, radial distribution function (RDF), lattice parameter, and the average number of hydrogen bonds between water–water molecules are evaluated by employing MD strategy. According to the potential energy results, the order for the water models in both TBAB and TBPB hydrate stabilities is as follows: TIP4P/Ice > TIP4P ≈ SPC > TIP3P. This order agrees well with the previous studies of gas hydrates and ices. In the absence and presence of methane and carbon dioxide guest molecules, the height of the peaks in the RDF of oxygen–oxygen atoms decreases with lowering pressure and increasing temperature; greater MSD, diffusion coefficient, and lattice parameter values are also achieved. Thus, in the absence and/or presence of guest gas molecules, the stability of TBAB and TBPB hydrate cages decreases with increasing temperature and reducing pressure. A good match is noticed between the results of MD simulation and previous experimental and theoretical studies, confirming the accuracy and validation of the simulation method. Reduction of the hydrogen bond balance between water molecules and formation of new hydrogen bonds between the water and the hydroxyl groups of methanol and/or ethanol molecules in the cages indicate that methanol and ethanol molecules have an inhibitory effect on TBAB and TBPB hydrates. Due to different hydrophilic versus hydrophobic behaviors of alcohols, the extent of disruption of hydrogen bonds between water–water molecules of TBAB and TBPB hydrates in the presence of methanol is larger than that in the presence of ethanol, which is consistent with the MD simulation results of clathrate hydrate. This study can help to further understand the semiclathrate hydrate stability or dissociation conditions at a molecular scale for better design and operation of corresponding processes.

Coupling Molecular Dynamics and Direct Simulation Monte Carlo using a general and high-performance code coupling library

A domain-decomposed method to simultaneously couple the classical Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC) methods is proposed. This approach utilises the MPI-based general coupling library, the Multiscale Universal Interface. The method provides a direct coupling strategy and utilises two OpenFOAM based solvers, mdFoam+ and dsmcFoam+, enabling scenarios where both solvers assume one discrete particle is equal to one molecule or atom. The ultimate goal of this work is to enable complex multi-scale simulations involving micro, meso and macroscopic elements, as found with problems like evaporation.Results are presented to show the fundamental capabilities of the method in terms of mass and kinetic energy conservation between simulation regions handled by the different solvers. We demonstrate the capability of the method by deploying onto a large supercomputing resource, with attention paid to the scalability for a canonical NVT ensemble (a constant number of atoms N, constant volume V and constant temperature T) of Argon atoms. The results show that the method performs as expected in terms of mass conservation and the solution is also shown to scale reasonably on a supercomputing resource, within the known performance limits of the coupled codes. The wider future of this work is also considered, with focus placed on the next steps to expand the capabilities of the methodology to allow for indirect coupling (where the coarse-graining capability of the DSMC method is used), as well as how this will then fit into a larger coupled framework to allow a complete micro-meso-macro approach to be tackled.

Prediction of mechanical properties of EPON 862 (DGEBF) cross-linked with curing agent (TETA) and SiO2 nanoparticle based on materials studio

The present study focuses on the prediction of mechanical properties of SiO2 nanocluster reinforced epoxy resin (DGEBF) cross-linked with curing agent W (TETA). The MD models of the reinforced epoxy were built using the amorphous module of Material Studio 7.0 (Accelrys Inc.). The mechanical properties of this cross-linked structure were determined using MD simulations. SiO2 qurtiz with different aspect ratios of weight percent (6%, 8% and 10%) in order to construct amorphous unit cells of SiO2-Epoxy nanocomposites. The SiO2-Epoxy nanocomposites system undergoes NPT (constant number of atoms, pressure and temperature) ensemble with applied uniform strain field during MD simulation to obtain density curve, cell size diagram and the results file.

INVESTIGATING THE ROLE OF MOLECULAR INTERACTIONS IN POLYMORPHISM OF MEFENAMIC ACID IN ETHYL ACETATE SOLUTION

Mefenamic acid, a widely used nonsteroidal anti-inflammatory and analgesic agent, is one of the active pharmaceutical ingredients that exhibit polymorphisms. This study reports a combined experimental and molecular dynamics simulation study of mefenamic acid crystallization in ethyl acetate. The solid-state characterization of the polymorph produced using Fourier transform infrared spectroscopy (FTIR), X-Ray powder diffractometer (XPRD), and differential scanning calorimetry (DSC) analysis show the characteristic of Form I, which were N-H stretching at 3313cm-1, two endothermic peaks, and significant XPRD peaks at 6.3°, 13.8°, 15.9°, 21.3°, and 26.3°. The molecular dynamics simulations were performed using COMPASS force field available in the Material Studio 5.5 simulation package. The simulations were run for equilibration with a time step of 1 fs for a period of 250 ps and 2000 ps simulation in NVE (constant number of atoms, volume and energy) and NPT (constant number of atoms, pressure and temperature) thermodynamic ensemble, respectively. The trajectory files from the simulation were analyzed for radial distribution function (RDF) to investigate the intermolecular interactions. The simulation results showed strong solute-solute and solute-solvent interactions, which were O1MA•••H15MA and O1EA•••H15MA. These findings revealed the presence of hydrogen bonds that contributes to the solvation and formation of hydrogen motif in polymorphic Form I of mefenamic acid during crystallization with ethyl acetate as a solvent.

Molecular Dynamics Simulation and Characterization of Graphene–Cellulose Nanocomposites

The mechanical properties of graphene-cellulose (GC) nanocomposites are investigated using molecular dynamic (MD) simulations in this work. The influences of graphene concentrations, aspect ratios, and agglomeration on elastic constants and interfacial properties are reported. A polymer consistent force field (pcff) was used in the analysis. The GC nanocomposites system underwent NVT (constant number of atoms, volume, and temperature) and NPT (constant number of atoms, pressure, and temperature) ensemble with an applied uniform strain during the MD simulations. The stress-strain responses were evaluated for both randomly dispersed and stacked GC unit cell in order to study the effects of graphene concentrations, aspect ratio, and agglomeration on Young's modulus. The results indicate that Young's modulus of neat cellulose may be enhanced by incorporating graphene in the GC nanocomposites. It is observed that dispersed graphene shows a comparatively higher Young's modulus than the same with agglomerated graphene. The cohesive and pullout forces versus displacement data are reported under normal and shear modes. It is seen that both cohesive and pullout forces are enhanced for GC specimens with higher graphene aspect ratios due to enlarged surface/interfacial area. The MD simulation results show reasonable agreement with available experimental data.

Molecular Dynamic Simulation of Graphene Reinforced Nanocomposites for Evaluating Elastic Constants

The mechanical properties of graphene/cellulose (GC) nanocomposites have been investigated using molecular dynamics (MD) simulations. The influence of graphene concentrations and agglomeration on elastic constants is studied. A polymer consistent force field (pcff) is used in the analysis. An efficient time integration scheme was implied in calculating the force in each time step from the corresponding position and velocity of the atom. The GC nanocomposites system undergoes NVT (constant number of atoms, volume and temperature) and NPT (constant number of atoms, pressure and temperature) ensemble with an applied uniform strain during MD simulation. The stress-strain responses were evaluated for GC unit cell in order to study the effects of graphene concentrations and agglomeration on Young's modulus. The results show significant improvement in Young's modulus for the GC nanocomposites compared to neat cellulose. The MD simulation results show reasonable agreement with the micromechanics based model and available experimental data.

Thermal Properties for Bulk Silicon Based on the Determination of Relaxation Times Using Molecular Dynamics

Molecular dynamics simulations are performed to estimate acoustical and optical phonon relaxation times, dispersion relations, group velocities, and specific heat of silicon needed to solve the Boltzmann transport equation (BTE) at 300 K and 1000 K. The relaxation times are calculated from the temporal decay of the autocorrelation function of the fluctuation of total energy of each normal mode in the ⟨100⟩ family of directions, where the total energy of each mode is obtained from the normal mode decomposition of the motion of the silicon atoms over a period of time. Additionally, silicon dispersion relations are directly determined from the equipartition theorem obtained from the normal mode decomposition. The impact of the anharmonic nature of the potential energy function on the thermal expansion of the crystal is determined by computing the lattice parameter at the cited temperatures using a NPT (i.e., constant number of atoms, pressure, and temperature) ensemble, and are compared with experimental values reported in the literature and with those computed analytically using the quasiharmonic approximation. The dependence of the relaxation times with respect to the frequency is identified with two functions that follow the functional form of the relaxation time expressions reported in the literature. From these functions a simplified version of relaxation times for each normal mode is extracted. Properties, such as group and phase velocities, thermal conductivity, and mean free path, needed to further develop a methodology for the thermal analysis of electronic devices (i.e., from nano- to macroscales) are determined once the relaxation times and dispersion relations are obtained. The thermal properties are validated by comparing the BTE-based thermal conductivity against the predictions obtained from the Green–Kubo method. It is found that the relaxation times closely resemble the ones obtained from perturbation theory at high temperatures; the contribution to the thermal conductivity of the transverse acoustic, longitudinal acoustic, and longitudinal optical modes being approximately 30%, 60%, and 10%, respectively, and the contribution of the transverse optical mode negligible.

Standard deviations of composition measurements in atom probe analyses—Part II: 3D atom probe

In a companion paper [F. Danoix, G. Grancher, A. Bostel, D. Blavette, Surf. Interface Anal. this issue (previous paper).], the derivation of variances of the estimates of measured composition, and the underlying hypotheses, have been revisited in the the case of conventional one dimensional (1D) atom probes. In this second paper, we will concentrate on the analytical derivation of the variance when the estimate of composition is obtained from a 3D atom probe. As will be discussed, when the position information is available, compositions can be derived either from constant number of atoms, or from constant volume, blocks. The analytical treatment in the first case is identical to the one developed for conventional 1D instruments, and will not be discussed further in this paper. Conversely, in the second case, the analytical treatment is different, as well as the formula of the variance. In particular, it will be shown that the detection efficiency plays an important role in the determination of the variance.

Effect of different treatments of long‐range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer

The present study analyzes the effect of the simulation conditions on the results of molecular dynamics simulations of G-protein coupled receptors (GPCRs) performed with an explicit lipid bilayer. Accordingly, the present work reports the analysis of different simulations of bovine rhodopsin embedded in a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer using two different sampling conditions and two different approaches for the treatment of long-range electrostatic interactions. Specifically, sampling was carried out either by using the statistical ensembles NVT or NPT (constant number of atoms, a pressure of 1 atm in all directions and fixed temperature), and the electrostatic interactions were treated either by using a twin-cutoff, or the particle mesh Ewald summation method (PME). The results of the present study suggest that the use of the NPT ensemble in combination with the PME method provide more realistic simulations. The use of NPT during the equilibration avoids the need of an a priori estimation of the box dimensions, giving the correct area per lipid. However, once the system is equilibrated, the simulations are irrespective of the sampling conditions used. The use of an electrostatic cutoff induces artifacts on both lipid thickness and the ion distribution, but has no direct effect on the protein and water molecules.

Molecular modeling of water structure in nano-pores between brucite (001) surfaces

Molecular dynamics (MD) computer simulations of liquid water held in one-dimensional nano-confinement by two parallel, electrostatically neutral but hydrophilic surfaces of brucite, Mg(OH) 2, provide greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural ordering, hydrogen bond (H-bond) organization, and local density of H 2O molecules at this important model hydroxide surface. NVT-ensemble MD simulations (i.e., at constant number of atoms, volume and temperature) were performed for a series of model systems consisting of 3 to 30 Å-thick water layers (containing 35 to 360 H 2O molecules) confined between two 19 Å-thick brucite substrate layers. The results show that the hydrophilic substrate significantly influences the near-surface water structure, with both H-bond donation to the surface oxygen atoms and H-bond acceptance from the surface hydrogen atoms in the first surface layer of H 2O molecules playing key roles. Profiles of oxygen and hydrogen atomic density and H 2O dipole orientation show significant deviation from the corresponding structural properties of bulk water to distances as large as 15 Å (∼5 molecular water layers) from the surface, with the local structural environment varying significantly with the distance from the surface. The water molecules in the first layer at about 2.45 Å from the surface have a two-dimensional hexagonal arrangement parallel to brucite layers, reflecting the brucite surface structure, have total nearest neighbor coordinations of 5 or 6, and are significantly limited in their position and orientation. The greatest degree of the tetrahedral (ice-like) ordering occurs at about 4 Å from the surface. The translational and orientational ordering of H 2O molecules in layers further from the surface become progressively more similar to those of bulk liquid water. A quantitative statistical analysis of the MD-generated instantaneous molecular configurations in terms of local density, molecular orientation, nearest neighbor coordination, and the structural details of the H-bonding network shows that the local structure of interfacial water at the brucite surface results from a combination of “hard wall” (geometric and confinement) effects, highly directional H-bonding, and thermal motion. This structure does not resemble that of bulk water at ambient conditions or at elevated or reduced temperature, but shares some similarities with that of water under higher pressure.

Melting in confined systems: Monte Carlo simulations of Kr in nano-pores of MCM-41

Melting of krypton confined in 4 nm MCM-41 pore has been studied. A continuous melting, starting from the pore center, has been observed in various thermodynamic conditions: along the saturation line, at constant pressure and at constant number of atoms. The crucial role of the atom–wall interaction has been discussed, particularly its influence on an increase or a reduction of the melting temperature.

Simulation of orientation of uniaxially stretched poly(vinyl phenol) by molecular dynamics

AbstractMolecular dynamics were performed for the simulation of the uniaxial deformation of poly(vinyl phenol) under periodic boundary conditions with the Parrinello–Rahman scheme followed by relaxation under NVT conditions (constant number of atoms, volume, and temperature). Changes in the orientation of the main chain, benzene segments, and hydrogen bonds were analyzed with the second‐order Legendre polynomial, 〈P2(cos θ)〉. Conformational changes were also followed. During deformation, backbone and phenyl rings both initially orient parallel to the draw direction. After relaxation, the chain is oriented parallel to the deformation direction, and side groups orient approximately perpendicular to this direction, in agreement with experimental data reported in the literature. Orientation values are higher than experimental values, as expected from the limited relaxation time range attainable in the simulations. Deformation proceeds by changes from gauche conformers to nontrans, nongauche, and trans conformers, whereas relaxation mainly allows high‐energy nontrans, nongauche conformers to convert into lower energy trans conformers. Values of the α angle for ring and bonded OH segments agree with those in the literature. Differences observed for free hydroxyl moieties are discussed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1601–1625, 2002

Overall connectivities/topological complexities: a new powerful tool for QSPR/QSAR

Earlier attempts to assess the complexity of molecules are analyzed and summarized in a number of definitions of general and topological complexity. A concept which specifies topological complexity as overall connectivity, and generalizes the idea of molecular connectivities of Randic, Kier, and Hall, is presented. Two overall connectivity indices, TC and TC1, are defined as the connectivity (the sum of the vertex degrees) of all connected subgraphs in the molecular graph. The contributions to TC and TC1, which originate from all subgraphs having the same number of edges e, form two sets of eth-order overall connectivities, eTC and eTC1. The total number of subgraphs K is also analyzed as a complexity measure, and the vector of its eth-order components, eK, is examined as well. The TC, TC1, and K indices match very well the increase in molecular complexity with the increase in the number of atoms and, at a constant number of atoms, with the increased degree of branching and cyclicity of the molecular skeleton, as well as with the multiplicity of bonds and the presence of heteroatoms. The potential of the three sets of eth-order complexities for applications to QSPR was tested by the modeling of 10 alkane properties (boiling point, critical temperature, critical pressure, critical volume, molar volume, molecular refraction, heat of formation, heat of vaporization, heat of atomization, and surface tension), in parallel with Kier and Hall's molecular connectivity indices (k)chi. The topological complexity indices were shown to outperform molecular connectivity indices in 44 out of the 50 pairs of models compared, including all models with four and five parameters.

Novel Indices for the Topological Complexity of Molecules

The development of molecular complexity measures is reviewed. Two novel sets of indices termed topological complexities are introduced proceeding from the idea that topological complexity increases with the overall connectivity of the molecular graph. The latter is assessed as the connectivity of all connected subgraphs in the molecular graph, including the graph itself. First-order, second-order, third-order, etc., topological complexities i TC are defined as the sum of the vertex degrees in the connected subgraphs with one, two, three, etc., edges, respectively. Zero-order complexity is also specified for the simplest subgraphs–the graph vertices. The overall topological complexity TC is then defined as the sum of the complexities of all orders. These new indices mirror the increase in complexity with the increase in the number of atoms and, at a constant number of atoms, with the increase in molecular branching and cyclicity. Topological complexities compare favorably to molecular connectivities of Kier and Hall, as demonstrated in detail for the classical QSPR test-the boiling points of alkanes. Related to the wide application of molecular connectivities to QSAR studies, a similar importance of the new indices is anticipated.