Atomic Distribution Function Research Articles

Transport properties of zwitterion glycine, diglycine, and triglycine in water

Diffusion, transport of mass in response to concentration and thermal energy gradient, is an important transport property, vital in material science and life science. In the present work, we have studied about the diffusion of zwitterion glycine, zwitterion diglycine and zwitterion triglycine in SPC/E model of water using classical molecular dynamics. Self and binary diffusion coefficients of aqueous solution of these molecules have been estimated using Einstein’s method. Our results agree with experimental data reported in literatures. Temperature dependency of diffusion of glycine in water has been explored using estimated values of self and binary diffusion coefficients at four different temperature. Effects of peptide bond formation in diffusion has been studied using peptide chain composed of up to three monomers of glycine. The system-size dependence of diffusion coefficient has been studied and the shear viscosity of solvent and system has been calculated. Also, the diffusion coefficient of zwitterion glycine in other water model TIP4P/2005 has been estimated. The structure of the system has been analyzed using radial distribution function of different atoms.

Effect of Water on the Structural Transformations in the Interfacial and Drainage Layers of Semipermeable Composite Membranes

Air-dry and water-saturated samples of UAM-50 and UAM-100 composite membranes were studied by X-ray diffractomery (XRD) and differential scanning calorimetry (DSC). A full-profile analysis of the diffraction patterns was performed, and the radial distribution functions (RDFs) of atoms in the drainage layer were constructed. The RDFs generally illustrate the relationship with the geometry of the structure of the air-dry and water-saturated samples. The additional peak with the radii r3 = 6.18 A and r3 = 6.44 A with small coordination numbers in the water-saturated samples suggests that the interplanar space d (hk0) contains the atoms of the water molecules. It was found that water reduces the X-ray crystallinity by 26% in the UAM-50 sample and by 36% in UAM-100. According to the DSC data, an interfacial layer appears at the interface; the DSC curves of the water-saturated samples in the temperature range 125–226°C show an exothermal effect with ΔН = 20.7 kJ/kg for UAM-50 and ΔН = 27.95 kJ/kg for UAM-100, which indicates hydration of the polar groups of cellulose acetate and polyamide in the interfacial layer of the composite films.

Argentite-Acanthite Transformation in Silver Sulfide as a Disorder-Order Transition

An alternative model has been proposed for the phase transition from cubic argentite s-Ag2S to monoclinic acanthite α-Ag2S in silver sulfide as a disorder–order transition. It has been shown that, as the temperature decreases below the transition temperature Ttrans, S atoms equiprobably occupying the sites of the body centered cubic (bcc) nonmetal sublattice of argentite are concentrated at four sites of the monoclinic nonmetal sublattice, whereas the other sites remain vacant. A disorder-order transition channel including three superstructure vectors of k9 and k4 stars has been determined. The distribution function of sulfur atoms in monoclinic acanthite α-Ag2S has been calculated. It has been shown that displacements of sulfur atoms distort the bcc nonmetal sublattice of argentite, forming a monoclinic lattice, where silver atoms are spaced by quite large distances and occupy their crystallographic positions with a probability of 1. The region of allowed values of the long-range order parameters η9 and η4 for the model monoclinic ordered phase α-Ag2S has been determined.

Atomistic modeling of heat treatment processes for tuning the mechanical properties of disordered solids

We investigate the effect of a single heat treatment cycle on the potential energy states and mechanical properties of metallic glasses using molecular dynamics simulations. We consider the three-dimensional binary mixture, which was initially cooled with a computationally slow rate from the liquid state to the solid phase at a temperature well below the glass transition. It was found that a cycle of heating and cooling can relocate the glass to either rejuvenated or relaxed states, depending on the maximum temperature and the loading period. Thus, the lowest potential energy is attained after a cycle with the maximum temperature slightly below the glass transition temperature and the effective cooling rate slower than the initial annealing rate. In contrast, the degree of rejuvenation increases when the maximum temperature becomes greater than the glass transition temperature and the loading period is sufficiently small. It was further shown that the variation of the potential energy is inversely related to the dependence of the elastic modulus and the yield stress as functions of the maximum loading temperature. In addition, the heat treatment process causes subtle changes in the shape of the radial distribution function of small atoms. These results are important for optimization of thermal and mechanical processing of metallic glasses with predetermined properties.

Analysis of the atomic structure of the amorphous metal alloy Al84Ni6La10

The paper presents an analysis of the atomic radial distribution function of the amorphous metal alloy Al84Ni6La10 based on the fragmentary model. A comparative analysis of the most probable interatomic distances in the alloy and its compounds demonstrated the presence of crystalline nuclei of the following phases: Al3La, AlNi3, Al4La and Al. The crystalline nuclei of the Al4La compound are the smallest (~7-8 Å), while the minimal size of the most nuclei of the other phases is 1-1.5 nm. The following phases were observed in the crystallised alloy: Al11La3, Al3Ni, and Al.

New insights into methane hydrate dissociation: Utilization of molecular dynamics strategy

Hydrate reserves play a crucial role in energy storage and resources across the world. Gas hydrate formation may lead to various forms of blockages in oil/gas production and transportation processes, resulting in high capital and operating costs. Hence, it is important to determine the methane hydrate formation conditions and to understand the vital process and thermodynamic parameters. In this study, molecular dynamic (MD) simulations are conducted to investigate the microscopic mechanisms/phenomena and intermolecular forces involved in methane hydrate decomposition, where molecular interactions, structures, and behaviours need to be appropriately determined/selected. Through a systematic parametric sensitivity analysis, the impacts of temperature, pressure, and cage occupancy on hydrate dissociation are studied. Furthermore, the diffusion coefficient, density, and heat capacity of the methane hydrates are determined by employing MD strategy. The stability of water cages is examined at various decomposition times, temperatures, and pressures. According to the radial distribution function and mean square displacement of oxygen-oxygen and carbon-carbon atoms, the stability of hydrate cages decreases with increasing temperature, while it increases with increasing the cage occupancy and pressure. The addition of inhibitors (e.g., methanol) to small cavities in the hydrate structure creates new hydrogen bonds between the water and inhibitor molecules in the cages, accelerating the decomposition of hydrates. A good agreement is noticed between the outcomes of this research work and the results obtained in experimental and theoretical studies available in the literature. Analysing the outcome of the present and previous research works, the current study provides new reliable/logical information on the molecular level of the hydrate dissociation process. It is expected that such a research investigation offers effective tips/guidelines to deal with hydrate formation and dissociation in terms of utilization, prevention, and processing.

X-Ray Diffraction and Differential Scanning Calorimetry Studies of Crystalline and Amorphous Regions in Composite Porous Films

A comparative analysis of the structural evolution of MGA-95 and ESPA1 polymer composite porous films is performed by plotting the radial distribution functions of atoms using empirical X-ray scattering intensity curves and the thermophysical parameters of melting are calculated using data from differential scanning calorimetry (DSC). In the case of the water-saturated MGA-95 sample, the atomic density in the first coordination sphere of the cellulose acetate macromolecule is shown to decrease due to the breaking of intramolecular hydrogen bonds. The atomic density of coordination spheres with radii corresponding to the lattice parameters decreased suggesting spatial disorder of the macromolecules. The DSC data for the MGA-95 film (the enthalpies of melting of the dry and water saturated samples are ΔH = 8.57 and 6.55 J/g, respectively) suggests that sorption of water molecules leads to a decrease in the degree of crystallinity due to a change in the crystalline fractions in the polycrystals. In the case of the ESPA1 composite film, a decrease in the radius and an increase in the atomic density of the first coordination sphere are indicative of the orientational disorder of amorphous phase molecules upon the sorption of water. The appearance of additional coordination spheres with R2 = 3.88 and R3 = 5.26 A in the swollen ESPA1 sample suggests the quantitative redistribution of crystal phases in the substrate material. A detailed analysis of endothermic peaks on the DSC curve shows that the ratio of low- and high-temperature phases varies from 64% : 36% in the dry sample up to 51% : 49% in the water saturated sample at almost identical enthalpies of melting of ΔH = 12.18 and 11.66 J/g, respectively.

Retraction Note to: MD simulations on the melting and compression of C, SiC and Si nanotubes

By the Tersoff potential based molecular dynamics (MD) method, the melting and axial compression of the (5,5) C, SiC, and Si nanotubes are simulated, and their molecular configurations, atomic radial distribution functions (RDF) and energy changes during heating-up, as well as their compressive force–strain curves, are obtained. According to the computed results, the differences of the melting and compressive mechanical properties of the three nanotubes are discussed. It is found that the melting C, SiC, and Si nanotubes have netlike, loose spherical and compact spherical configurations respectively, and that the C nanotube has the highest melting point, specific heat, melting heat and load support capability, whereas the Si nanotube has the lowest ones.

Polarizable force field for molecular dynamics simulations of silver nanoparticles

Contact of silver metal surfaces with water, ions and organic ligands experiences induced charges, leading to attractive polarization. These forces play an important role at inorganic/organic interfaces and complement other non-bonded surface interactions. Despite the importance of these interactions, it, however, remains difficult to implement polarization effects to classical molecular dynamics (MD) simulations. In this contribution, we first present an overview of two popular polarizable models, such as Drude oscillator and the rigid rod model, which are utilized to mimic the polarizability of bulk metals. Second, we implemented the rigid rod model to the polarizable force field (FF) for a silver atom, which was further adapted for atomistic MD simulations of silver nanoparticles (AgNPs) composed of 1397 atoms. In our model, induced charge polarization is represented by the displacement of a charge-carrying virtual site attached rigidly to an original Ag atom. To explore the role of polarization, we compared the performance of the classical nonpolarizable FF and the new polarizable model in the MD simulations of adsorption of water and ions onto quasi-spherical AgNP and the flat crystalline silver surface. The analysis of the radial distribution function of Ag-Ag atoms demonstrated that the introduction of the polarization effect had minor effects on face-centered cubic (fcc) packing of silver atoms of bare and water-solvated AgNPs. We found that the polarizable FF causes some increase in attractive interactions between the silver surface and water molecules and Na+ ions. As a crucial test of the developed polarizable model, the structure of adsorbed interfacial water molecules was analyzed. Our data suggest that the environment-induced polarization of the silver surface contributes significantly to the structure of adsorbed interfacial water layers and it also plays an important role in the adsorption of positive ions. However, it was also found out that the polarization effect has a rather short-range effect, so that a minor contribution of silver polarization was seen for adsorption of water molecules and ions from distant solvation shells.

Chemical Ordering in Ni66.7 In33.3 Liquid Alloy

Short range order structure of liquid Ni66,7In33,3 alloy has been studied by means of X-ray diffraction method at temperatures 1235; 1260 and 1335 K. Experimental structure factors and radial atomic distribution function are analyzed. It is shown that structure of Ni66,7In33,3 in liquid state reveals chemical ordering, like to Ni2In type structure

Probing Atomic Distributions in Mono- and Bimetallic Nanoparticles by Supervised Machine Learning.

Properties of mono- and bimetallic metal nanoparticles (NPs) may depend strongly on their compositional, structural (or geometrical) attributes, and their atomic dynamics, all of which can be efficiently described by a partial radial distribution function (PRDF) of metal atoms. For NPs that are several nanometers in size, finite size effects may play a role in determining crystalline order, interatomic distances, and particle shape. Bimetallic NPs may also have different compositional distributions than bulk materials. These factors all render the determination of PRDFs challenging. Here extended X-ray absorption fine structure (EXAFS) spectroscopy, molecular dynamics simulations, and supervised machine learning (artificial neural-network) method are combined to extract PRDFs directly from experimental data. By applying this method to several systems of Pt and PdAu NPs, we demonstrate the finite size effects on the nearest neighbor distributions, bond dynamics, and alloying motifs in mono- and bimetallic particles and establish the generality of this approach.

Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 A from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.

The effect of different alcohols on the Asp23-Lys28 and Asp23-Ala42 salt bridges of the most effective peptide in Alzheimer's disease: Molecular dynamics viewpoints

The beta-amyloid peptide Aβ1-42 is the most effective peptide in the process of forming plaque and creating Alzheimer's. After the separation of Aβ1-42 from APP membrane protein, the membrane surface is transmitted to the extracellular environment, which is a crowded environment. On the other hand, stability of salt bridges Asp23-Lys28 and Lys28-Ala42 is important for monomer toxicity and fibrillation formation. In this work, the effects of ethanol, propanol, butanol, pentanol, hexanol, heptanol and octanol on the Asp23-Lys28 and Lys28-Ala42 salt bridges of the Aβ1-42 have been investigated by molecular dynamics simulation. The radial distribution function of the oxygen atoms of the water around the atoms Cγ-Asp23, Nξ-Lys28 and O-Ala42 was calculated in the presence of the alcohols. The results show that the peak height of the radial distribution function around the Cγ-Asp23 atom is larger than the other two atoms. Also, the numbering of water molecules in the interval corresponding to the first peak in the radial distribution function for all atoms involved in the two salt bridges Asp23-Lys28 and Lys28-Ala42 was calculated. The results show that the obtained coordinate numbers are within the range of experimental numbers reported for water. The results also show that the order of water molecules around the O-Ala42 is lower. The results of solvent accessible surface area of Aβ1-42 show that the Lys28-Ala42 Salt bridge stability is more important for toxicity of monomer.

Study of Three-Dimensional, Surface, and Linear Structures of Allotropic Carbon: Diffraction Spectra of Auger Electron Energy Losses

A theoretical approach is developed for determining the parameters of nanoscale crystal structures using diffraction spectra of Auger electron energy losses. The approach is based on modeling the radial distribution functions of atoms while allowing for the sizes of atomic structures, and on the geometry of surfaces of three-dimensional, surface, and linear objects intersecting with a sphere. Using the example of allotropic carbon phases, it is shown that the proposed technique allows assessment of a studied object’s thickness and the depth of the analyzed signal output with an accuracy of one atom’s diameter.

Atomic Structure of the Amorphous Metallic Alloy Al83.5Ni9.5Si1.4La5.6

The atomic structure of the amorphous metallic alloy Al83.5Ni9.5Si1.4La5.6 is investigated based on the analysis of the experimental atomic radial distribution function (ARDF) in the fragmentary model. A comparative analysis of the most probable interatomic distances in the alloy and possible compounds based on it has demonstrated the presence of crystalline nuclei of the following phases: Al3La, Al3Ni, Al2.12La0.88, Al3Ni5, and Al. The largest ones (1–2 nm) are nuclei of the Al3Ni and Al compound, while the majority nuclei of all the other phases had sizes of about 7 A. Al and Al3Ni, as well as Al11La3 and Al5.56LaNi1.44 are observed in the crystallized alloy.

A comparative study of aqueous DMSO mixtures by computer simulations and integral equation theories

ABSTRACTSeveral computer simulation studies of aqueous-dimethylsulfoxide with different force field models, and conducted by different authors, point out to an anomalous depressing of second and third neighbour correlations of the water–water radial distribution functions. This seemingly universal feature can be interpreted as the formation of linear water clusters. We test here the ability of liquid state integral equation theories to reproduce this feature. It is found that the incorporation of the water bridge diagram function is required to reproduce this feature. These theories are generally unable to properly reproduce atom–atom distribution functions. However, the near-ideal Kirkwood–Buff integrals are relatively well reproduced. We compute the X-ray scattering function and compare with available experimental results, with the particular focus to explain why these data do not reproduce the cluster pre-peak observed in the water–water structure factor.

Microscopic modeling of gas-surface scattering: II. Application to argon atom adsorption on a platinum (111) surface

A new combination of first principle molecular dynamics (MD) simulations with a rate equation model presented in the preceding paper (paper I) is applied to analyze in detail the scattering of argon atoms from a platinum (111) surface. The combined model is based on a classification of all atom trajectories according to their energies into trapped, quasi-trapped and scattering states. The number of particles in each of the three classes obeys coupled rate equations. The coefficients in the rate equations are the transition probabilities between these states which are obtained from MD simulations. While these rates are generally time-dependent, after a characteristic time scale tE of several tens of picoseconds they become stationary allowing for a rather simple analysis. Here, we investigate this time scale by analyzing in detail the temporal evolution of the energy distribution functions of the adsorbate atoms. We separately study the energy loss distribution function of the atoms and the distribution function of in-plane and perpendicular energy components. Further, we compute the sticking probability of argon atoms as a function of incident energy, angle and lattice temperature. Our model is important for plasma-surface modeling as it allows to extend accurate simulations to longer time scales.

Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy.

The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its insitu changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.

The influence of moisture content on methane adsorption in lignite: A molecular simulation study

As a high-efficiency clean energy and chemical raw material, coal-bed methane (CBM) has received wide attention in recent decades. At the present stage, new strategy to achieve a breakthrough in the CBM exploration and development is regarded as the primary goal for China’s lignite region. Usually, lignite contains a high moisture content in our country. Therefore, it is of great practical significance to understand the effect of moisture content on methane adsorption in lignite. Herein, molecular simulations of Monte Carlo and molecular dynamics methods are employed to elucidate this effect on methane adsorption with three moisture contents of 0%, 1.6% and 3.2%, and three temperatures of 298 K, 313 K and 373 K and the pressure range of 0–10 MPa are considered in the work. The lignite substrate model is composed of an aromatic skeleton amorphous structure with 88 atoms, including carbon, hydrogen, oxygen, nitrogen and sulfur. The adsorption amount, adsorption heat, and atomic radial distribution function along N, O, and S atoms are investigated in turns. The results show that the adsorption amount of methane decreases with the increase of moisture content in lignite, because the water molecules would be superior to methane to occupy the adsorption sites in lignite at the initial stage. The adsorption amount of methane decreases with the increase of temperature due to the molecules thermaldynamic property. The adsorption heat of methane decreases with the increase of moisture content in lignite. In addition, the N and S atoms exhibit the stronger interactions with methane than the O atom in lignite. This molecular simulation results are not only helpful to understand the adsorption mechanism of methane in lignite, but also provide theoretical prediction and scientific evidence for the exploration of CBM.

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.