Atomic Radial Distribution Functions Research Articles

Study of the short-range order of Co-W alloys electrodeposited using pulse current

Pulsed electrodeposition modes allowed to obtain amorphous Co-W alloys. Using X-ray phase and spectral analysis methods, it was established that the deposition modes and the concentration of the amorphizing component (sodium tungstate salts) in an aqueous electrolyte solution affect the amorphization of alloys. The short-range atomic order was studied by X-ray diffraction analysis and the sizes of the regions of ordered arrangement of atoms were determined in X-ray amorphous Co-W alloys obtained by pulsed electrodeposition. The radial distribution function of atoms was analysed. The assumption is made that cobalt and tungsten atoms combine into configurations that are irregular polyhedrons.

Effect of Temperature on the Radial Distribution Function of Atoms in the Silicate Glass 2sio2·PBO

In this article, results of investigation of the effect of temperature on radial distribution function of atoms in lead-silicate glass are reported. Radial distribution functions of atoms in the lead-silicate glass 2SiO2∙PbO were calculated via Mathematica 5.1 Wolfram Research from high-temperature X-ray diffraction patterns. It turned out that in the range of 773-973 K mainly variations of the location of atoms in the third coordination sphere have observed, while in the range of 973-1123 K, changes in the first and second coordination spheres take place.

Structure and interactions in reline (1:2 Choline chloride – Urea mixture) according to quantum chemical calculations and molecular dynamics simulation

Quantum chemical calculations using the B3LYP + GD3/6–311++g(2d,2p) method were carried out to study the structure and interactions in a number of complexes containing a choline cation, a chloride anion and urea molecules. The contributions from Coulomb and van der Waals interactions were calculated. The QTAIM method was used to evaluate the strength of various bonds in these complexes. A molecular dynamics simulation of reline was also carried out in the NPT ensemble at a pressure of 1 atm and at temperatures of 298 and 323 K, with the GAFF force field and charges taken from our quantum chemical calculations. The particle radial distribution functions of centers of mass, local mole fraction functions, atom–atom radial distribution functions, and spatial distribution functions were calculated. Particles of different types were shown to form bonds of different types competing with each other.

Solvation structure and dynamics of favipiravir in supercritical CO2. A molecular dynamics investigation

The solvation structure and related dynamics of favipiravir diluted in supercritical CO2 in a wide density range (0.2–––2.0 ρc) along a near-critical isotherm (1.03 Tc) have been extensively studied by performing classical molecular dynamics simulations. The potential model of favipiravir developed in our previous studies was used in combination with the well-established EPM2 model of CO2 in the simulations. The results obtained have revealed that the local density augmentation of CO2 inside the first solvation shell of favipiravir is maximized at 0.67 ρc and is about 5.6 times larger than the corresponding value for pure supercritical CO2 at the same conditions. The local solvation structure around the favipiravir solute has also been investigated in terms of the atom–atom radial distribution functions. The intermittent residence dynamics of CO2 molecules in the first solvation shell of favipiravir, as well as the single translational and reorientational dynamics of favipiravir have also been investigated, revealing the important role of the local density augmentation of CO2 around the favipiravir solute upon these specific dynamic properties.* Corresponding authors.

Thermal Properties Investigation of FeCr Alloy Using Lammps Simulation: A Preliminary Study

At present, nuclear reactor technology that is widely used because of its proven reliability is the gen-III + nuclear reactor. Even if it is seen from the aspect of safety and reliability of this generation reactor, it has been proven, but because nuclear energy plays a vital role to meet the growing world energy needs, it is necessary to have a type of nuclear reactor that is tailored to those needs.The next generation of nuclear reactors must meet the requirements of fulfilling safety requirements, be flexible, a longer operating life (more than 60 years), more economical. In order for a reactor to produce higher power, a longer operating life and more economical, reactor structure materials which are capable of being operated at high temperatures are needed. The types of materials that are expected to meet these requirements include various types of ferritic / martensite steel, austenite, alloy steel containing nickel, and metal glass materials and ceramic materials. FeCr metal alloys are alloys that form the metals mentioned above, so it is important to conduct research both in simulation and experiment. Molecular Dynamics simulation of FeCr alloys using Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) has been done to explore their thermodynamic characteristics such as heat treatment, solubility of Cr, atomic radial distribution function (RDF). The results of the simulation are illustrated using Visual Molecular Dynamics (VMD) code.
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Fragmentary Model of the Atomic Structure of the Ion-Conducting Semiconductor Glass AgGeAsSe3

The atomic radial distribution function of vitreous AgGeAsSe3, obtained based on the experimental intensity curves taken with monochromatic copper and molybdenum radiation, is interpreted using a fragmentary model in the entire ordering region (~9 Å). It is shown that the glass consists of selenium and selenium-arsenic tetrahedra with germanium and silver atoms inside. The spatial arrangement of such tetrahedra in glass within the ordering region is similar to their arrangement in the GeAsSe and GeSe2 structures. It is proposed that the “openwork” structure of the fragments of these structures allows the movement of Ag+ ions (ionic conductivity) in vitreous AgGeAsSe3. Fragments of the structure of the ion-conducting compound Ag2Se are not found in the studied glass.

Non-Phenomenological Description of the Time-Resolved Emission in Solution with Quantum-Classical Vibronic Approaches-Application to Coumarin C153 in Methanol.

We report a joint experimental and theoretical work on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule is characterized by an intramolecular charge transfer thus leading to remarkable shifts of the time-resolved emission spectra, dictated by the methanol reorganization dynamics. We selected this system as a prototypical test case for the first application of a novel computational protocol aimed at the prediction of transient emission spectral shapes, including both vibronic and solvent effects, without applying any phenomenological broadening. It combines a recently developed quantum-classical approach, the adiabatic molecular dynamics generalized vertical Hessian method (Ad-MD|gVH), with nonequilibrium molecular dynamics simulations. For the steady-state spectra we show that the Ad-MD|gVH approach is able to reproduce quite accurately the spectral shapes and the Stokes shift, while a ∼0.15 eV error is found on the prediction of the solvent shift going from gas phase to methanol. The spectral shape of the time-resolved emission signals is, overall, well reproduced, although the simulated spectra are slightly too broad and asymmetric at low energies with respect to experiments. As far as the spectral shift is concerned, the calculated spectra from 4 ps to 100 ps are in excellent agreement with experiments, correctly predicting the end of the solvent reorganization after about 20 ps. On the other hand, before 4 ps solvent dynamics is predicted to be too fast in the simulations and, in the sub-ps timescale, the uncertainty due to the experimental time resolution (300 fs) makes the comparison less straightforward. Finally, analysis of the reorganization of the first solvation shell surrounding the excited solute, based on atomic radial distribution functions and orientational correlations, indicates a fast solvent response (≈100 fs) characterized by the strengthening of the carbonyl-methanol hydrogen bond interactions, followed by the solvent reorientation, occurring on the ps timescale, to maximize local dipolar interactions.

Endothelial Cell Behavior and Nitric Oxide Production on a-C:H:SiOx-Coated Ti-6Al-4V Substrate

This paper focuses on the surface modification of the Ti-6Al-4V alloy substrate via a-C:H:SiOx coating deposition. Research results concern the a-C:H:SiOx coating structure, investigated using transmission electron microscopy and in vitro endothelization to study the coating. Based on the analysis of the atomic radial distribution function, a model is proposed for the atomic short-range order structure of the a-C:H:SiOx coating, and chemical bonds (C-O, C-C, Si-C, Si-O, and Si-Si) are identified. It is shown that the a-C:H:SiOx coating does not possess prolonged cytotoxicity in relation to EA.hy926 endothelial cells. In vitro investigations showed that the adhesion, cell number, and nitric oxide production by EA.hy926 endothelial cells on the a-C:H:SiOx-coated Ti-6Al-4V substrate are significantly lower than those on the uncoated surface. The findings suggest that the a-C:H:SiOx coating can reduce the risk of endothelial cell hyperproliferation on implants and medical devices, including mechanical prosthetic heart valves, endovascular stents, and mechanical circulatory support devices.

Mobility of Dissolved Gases in Smectites under Saturated Conditions: Effects of Pore Size, Gas Types, Temperature, and Surface Interaction

In a nuclear waste repository, the corrosion of metals and the degradation of the organic material in the waste matrix can generate significant amounts of gases. These gases should be able to migrate through the multibarrier system to prevent a potential pressure build-up that could lead to a loss of barrier integrity. Smectite mineral particles form a tortuous pore network consisting of larger interparticle pores and narrow interlayer pores between the platelets of the smectite minerals. These pores are normally saturated with water, so one of the most important mechanisms for the transport of gases is diffusion. The diffusion of gases through the interparticle porosity depends on the distribution of gas molecules in the water-rich phase, their self-diffusion coefficients, and the tortuosity of the pore space. Classical molecular dynamics simulations were applied to study the mobility of gases (CO2, H2, CH4, He, and Ar) in Na-montmorillonite (Na-MMT) under saturated conditions. The simulations were used to estimate the gas diffusion coefficient (D) in saturated Na-MMT as a function of nanopore size and temperature. The temperature dependence of the diffusion coefficient was expressed by the Arrhenius equation for the activation energy (Ea). The predicted D values of gases were found to be sensitive to the pore size as the D values gradually increase with increasing pore size and asymptotically converge to the gas diffusion coefficient in bulk water. This behavior is also observed in the self-diffusion coefficients of water in Na-MMT. In general, H2 and He exhibit higher D values than Ar, CO2, and CH4. The predicted Ea values indicate that the confinement affects the activation energy. This effect is due to the structuring of the water molecules near the clay surface, which is more pronounced in the first two layers of water near the surface and decreases thereafter. Atomic density profiles and radial distribution functions obtained from the simulations show that the interaction of the gas with the liquid and the clay surface influences mobility. The obtained diffusion coefficient for different gases and slit pore size were parameterized with a single empirical relationship, which can be applied to macroscopic simulations of gas transport.

Hydrogen bond induced solvent ordering in aqueous poly (sodium p-styrenesulfonate)

Molecular dynamics simulations were used to investigate the structure and dynamics of the diffuse interphase in aqueous poly (sodium p-styrenesulfonate) (NaPSS). The effect of temperature and the distance between Sδ+Oδ– and Oδ–Hδ+ dipoles on the ordering of explicit solvent molecules were extensively studied. With an increase in temperature, the atomic radial distribution function indicated a reduced density of water in the immediate vicinity of SO3− groups and a slight increase in density afterward. Using the dipole radial distribution function, water molecules were classified into multiple layers on the basis of the distance between Sδ+Oδ– (PSS) and Oδ–Hδ+ (H2O) dipoles. Orientation of Oδ–Hδ+ around Sδ+Oδ–, influenced by coulombic interactions, resulted in a greater number of hydrogen bonds (H-bonds) and improved H-bond correlation function between adjacent layers. The altered H-bond dynamics were found to severely restrict the solvent mobility in the layer close to SO3− groups. While the number of inter-layer H-bonds was found to be a result of water orientation, the H-bond correlation function was dependent on the mobility of water molecules. Mean square displacement and autocorrelation of dipole radial distances were calculated to distinguish between inter- and intra-layer solvent mobility. Our results provide molecular-level insights into the structure and dynamics of solvent water molecules in the diffuse interphase with a polyelectrolyte.

Local intermolecular structure, hydrogen bonding and related dynamics in the liquid cis/trans N-methylformamide mixture: A density functional theory based Born-Oppenheimer molecular dynamics study

The local intermolecular structure and related dynamics in the liquid cis/trans N-methylformamide mixture at ambient temperature and density conditions have been systematically studied by employing Born-Oppenheimer molecular dynamics simulation techniques. Particular attention has been paid to the local structure around the cis- and trans- conformers and the formation and dynamics of hydrogen bonds with their closest neighbors. The calculated atom–atom radial distribution functions are in very good agreement with available experimental data and reveal the existence of different types of hydrogen bonding intermolecular interactions. The average number of hydrogen bonds formed by the cis- conformers is higher in comparison with the one corresponding to the trans- conformers. Moreover, the lifetimes of the hydrogen bonds formed in the liquid are longer when the cis- conformers participate in the bond formation, either as donors or acceptors. These findings clearly indicate that the local structural network around the cis- conformers in the liquid is more cohesive. The latter finding is also reflected in the slower reorientational dynamics of the cis- conformers and the low- and high-frequency region of the spectral densities of the atomic velocity time correlation functions. Finally, the calculated average dipole moments of the trans- and cis- conformers are significantly higher than their corresponding gas-phase values, signifying the importance of polarization effects in this particular polar liquid solvent.

Melting at Mg/Al interface in Mg–Al–Mg nanolayer by molecular dynamics simulations

The melting at the magnesium/aluminum (Mg/Al) interface is an essential step during the fabrications of Mg–Al structural materials and biomaterials. We carried out molecular dynamics simulations on the melting at the Mg/Al interface in a Mg–Al–Mg nanolayer via analyzing the changes of average atomic potential energy, Lindemann index, heat capacity, atomic density distribution and radial distribution function with temperature. The melting temperatures () of the nanolayer and the slabs near the interface are significantly sensitive to the heating rate () over the range of ≤ 4.0 K ps−1. The distance () range in which the interface affects the melting of the slabs is predicted to be (−98.2, 89.9) Å at if the interface is put at = 0 and Mg (Al) is located at the left (right) side of the interface. The of the Mg (Al) slab just near the interface (e.g. Å) is predicted to be 926.8 K (926.6 K) at with 36.9 K (37.1 K) below 963.7 K for the nanolayer. These results highlight the importance of regional research on the melting at an interface in the nanolayers consisting of two different metals.

Electron Diffraction Study of Phase Formation in Nano Layers of Cu-=SUB=-2-=/SUB=-Te-In-=SUB=-2-=/SUB=-Te-=SUB=-3-=/SUB=-, Cu-In-Te Systems and Short-Range Atomic Order in Amorphous CuIn-=SUB=-5-=/SUB=-Te-=SUB=-8-=/SUB=- Films

It is shown that with the simultaneous and sequential deposition of films of the Cu2Te-In2Te3 system, as well as copper, indium, and tellurium of the highest purity used as starting materials, ~99.999%, taken in the ratio Cu : In : Te = 1 : 5 : 8, regardless of the deposition order ternary compounds of the compositions CuInTe2, CuIn3Te5, and CuIn5Te8 in the crystalline state are distinguished. During vacuum condensation of films on single-crystal substrates NaCl, KCl and amorphous celluloid cooled by liquid nitrogen to 203 K, the resulting films obtained both by co-evaporation of binary compounds of the Cu2Te-In2Te3 system and by the synthesis of thin layers applied by Cu, In, Te are amorphous. For the first time in nanosized amorphous films of the composition CuIn5Te8, crystallizing in the tetragonal system with the periods of unit cells a=6.162 Angstrem, c=12.291 Angstrem, obtained both under normal conditions and under the influence of an external electric field with a strength of 500 V · cm-1, the structure of the short-range atomic order is established --- the number of nearest neighbors --- coordination numbers and radius of coordination spheres. It was revealed that in amorphous CuIn5Te8 films obtained under the influence of an external electric field, in which the matrices consist of tetrahedral and octahedral environments of atoms, in opposite to films that are formed outside the field, the number of nearest neighbors remains unchanged, the radius of coordination spheres and interatomic distances are somewhat are shortened. Keywords: phase formation, elektronogram, radial distribution function of atoms (RDFA), coherent electron scattering.

Multi-scale study water and ions transport in the cement-based materials:from molecular dynamics to random walk

The transport properties of water and ions play a key role in the durability of cement-based materials. However, little work has been done to study the diffusion behaviors of water and ions in a multi-scale view. Therefore, the current paper presented a multi-scale molecular dynamics fed random walk (MD-RW) simulation scheme for the purpose of obtaining the diffusion coefficients of water and ions in the calcium-silicate-hydrate (C–S–H) gel. At nanoscale, MD simulations were used to obtain the diffusion coefficients of water and ions in the C–S–H with nanopore size ranging from 0.5 nm to 5 nm since pore size has a crucial effect on the diffusion behavior of water and ions. Then these results were utilized as the input parameters for random walk simulation to scale the confining effect up and derive the effective diffusion coefficients of water and ions in the C–S–H gel at mesoscale. The results acquired from mean square displacement, atomic intensity distribution function and radial distribution function show that water molecules and Cl ions would form Ca–Cl, Ca–O ion-clustering and hydrogen bonds with C–S–H substrate which will restrict the transport of water molecules and Cl ions. In addition, with the size of gel pore increases from 0.5 nm to 5 nm, the diffusion coefficient of water increases from 0.016 to 1.85 × 10−9 m2 s−1 and the diffusion coefficient of Cl ions increases from 0.002 to 0.75 × 10−9 m2 s−1. In the random walk simulation, the diffusion coefficients of water and Cl ion were derived as 1.01 × 10−12 m2 s−1 and 1.2 × 10−13 m2 s−1 in the FCC packing model and 1.55 × 10−11 m2 s−1 and 1.77 × 10−12 m2 s−1 in the BCC packing model respectively, which reaches reasonable agreement with the previous studies results. Unlike traditional reverse methods which back-calculate these coefficients from macroscopic experimental results and hypothesized microstructure, this study presents the first bottom-up method deriving the transport properties of C–S–H gel directly from the physicochemical characteristics and microstructure, which has relevant significance for the study of concrete resistance to ion erosion and provides a basis for designing durable concrete.

Computer Simulation of the Semiconductor Nanoelectromechanical Systems AIIBIVAs2 Stability after Attosecond Impulse Exposure

The article deals with computer modeling of responses of multicomponent semiconductor nanoelectromechanical systems of arsenides to an attosecond radiation pulse at cryogenic (T1=77 K) and standard temperatures (T2=298 K). Kinetic curves of relaxation processes in ternary semiconductor nanolayers CdSiAs2, CdGeAs2, ZnSiAs2, ZnGeAs2, and nanolayers of variable composition CdSi1-xGex As2, ZnSi1-xGexAs2, Cd1-xZnxSiAs2 и Cd1-xZnxGeAs2 are obtained. This research reveals the differences in the average relaxation energy of nanolayers that depend on temperature and the amplitudes of energy fluctuations, and the time of reaching the plateau. A comparison with relaxation processes taking place at absolute zero temperatures is demonstrated. The radial distribution functions of atoms in the system before and after relaxation processes caused by impulsive action on the system of atoms in the semiconductor layer are considered. The modification of the peaks corresponding to the coordination spheres of atomic distribution depending on the composition of the nanolayer is described. The regularities of relaxation changes of the first order coordination spheres, as well as the regularities of relaxation destructions of the second and the third order coordination spheres at cryogenic and standard temperatures are revealed.

Effect of additive concentration on water solution under vacuum ambient: A molecular dynamics simulation study

In order to explore the effect of different concentrations of additives on aqueous solution in vacuum ambient, this paper uses molecular dynamics simulation method to study different concentrations of magnesium chloride (MgCl2) aqueous solution, ethylene glycol aqueous solution and nano iron oxide (nano-Fe3O4) aqueous solution. The radial distribution function of atoms, the water molecules’ self-diffusion coefficient and the type and number of hydrogen bonds are analyzed in detail. The dynamic behavior between water molecules and chloride and alcohol molecules in the solution is revealed. The results show that the additives affect the crystallization of the solution by inhibiting the self-diffusion rate of water molecules, and the iron oxide nanoclusters exhibit the most obvious behavior. Meanwhile, the added additives can also restrain the formation of hydrogen bonds between water molecules in solution. This suppresses the hydrogen bonds between two water molecules. At the same time, it reduces the diffusivity of water molecules. These effects weaken the tendency of water molecules to migrate to the nucleus, and can curb the nucleation and growth of ice crystals in the aqueous solution to a certain extent. This research will provide reference value in the selection of ice-making working fluid. Nano-iron oxide has better performance than MgCl2, and glycol solution is not conducive to vacuum ice making.

Molecular Dynamics Simulation of Phosphorus Trichloride (PCl3) and Phosphorus Triiodide (PI3) Liquids by Using the Force-fields Derived from a Quantum Chemical Approach

In this study, phosphorus trichloride (PCl3) and phosphorus triiodide (PI3) as the condensed inorganic materials were investigated based on the molecular dynamics simulation. To this purpose, molecular dynamics simulations were performed by applying force field parameters derived from the quantum chemistry approach. The potential energy data were computed at the B3LYP/6-31+G (d) and B3LYP/dgdzvpd levels of theory for different configurations of PCl3 and PI3, respectively. To determine force field parameters, a four-site all-atom force field model was used to correlate the potential energy data. Therefore, the force field parameters were applied to perform the molecular dynamics simulations. The MD simulations were performed to obtain the atomic number density, enthalpy, heat capacity, and radial distribution function in the NPT and NVT ensembles for PCl3 and PI3 dimers. There is a good consistency between the experimental data and simulation results over a wide range of experimental conditions.

Analysis of Interface Fusion Effect between Old and New Asphalt under Plant Mixing and Cold Recycling Mode Based on Molecular Dynamics Simulation.

Road construction consumes a lot of resources and produces a lot of waste and other pollutants. With the emergence of a resource and energy crisis, how to make efficient use of rap has become the research focus of scientific researchers. The interface fusion effect of old and new asphalt in plant mixing and cooling recycling mode is analyzed in order to improve the utilization rate of old asphalt in reclaimed asphalt pavement. In this paper, Materials Studio software was used to establish a bitumen model using the method of four components of bitumen, and then the rationality of the model was verified by density, solubility number and atomic radial distribution function, and the diffusion coefficient obtained from the mean square displacement (MSD) was taken as its evaluation index. The results showed that the diffusion model tends to be stable after 20 ps, and the degree of diffusion increases with the increase in temperature. The degree of diffusion of new asphalt to old asphalt and the degree of diffusion of old asphalt to new asphalt are basically very similar; however, there are some differences at different temperatures. Only a small part of the surface contact between old and new asphalt has been fused, which accords with the partial fusion theory. Compared with Panjin 90# asphalt, the diffusion coefficient of Zhonghaiyou asphalt increases faster with the increase in temperature. The diffusion coefficient increases by 64.3% with the increase of the content of rejuvenators after adding different rejuvenators into the new asphalt. Clarifying the interface fusion effect will be helpful to guide the optimization design of cold-mixing recycled asphalt mixture more scientifically and reasonably. Future research should focus on increasing the fusion effect of old and new asphalt, and explore its influence on the conventional road performance of asphalt mixture.

Application of fragmentary model to analysis of the atomic structure of amorphous materials

Experimental atomic radial distribution functions, obtained from diffraction amorphous materials, are proposed to be interpreted using the model curves built upon the complete structural data of crystal analogues or upon the separate fragments of their structure. This modelling technique is called a fragmentary model. A model atomic radial distribution function is a radial cross section of the spherically symmetric function of interatomic distances. It characterises a nanodispersed diffraction amorphous polycrystal as uniquely as the values of interplanar spacings and intensities characterise a regular polycrystal. Comparing the model and experimental atomic radial distribution functions by the maxima positions we can perform the “identification” and “phase analysis” of nanodispersed diffraction amorphous polycrystals and define the crystalline compounds whose fragments form the structure of glass.

The study of structure and interactions of glucose-based natural deep eutectic solvents by molecular dynamics simulation

In the current study, molecular dynamics simulations were conducted to investigate the structural and dynamical properties of glucose-based Deep Eutectic Solvents (DESs) at different molar ratios (the mixture of glucose and choline chloride with the molar ratios of 1:3, 1:1 and 3:1). Accordingly, the interaction energies of different species and structural properties such as atom–atom radial distribution functions (RDFs), the hydrogen-bonding network between species, and spatial distribution functions (SDFs) were computed to understand effective interactions in the eutectic mixture formation. It was found that the insertion of glucose molecules reduced the accumulation of chloride anions around choline cations, eventually decreasing the interaction between the choline chloride ion pairs. Moreover, the possible explanations for the thermos-physical properties of DESs, such as the shear viscosity and density, have been provided. Dynamical properties of DES were evaluated by calculating the mean-square displacement (MSD) and the velocity autocorrelation function (VACF) for the centers of the mass of the ions and glucose molecules. MSD analysis results were then used to calculate the self-diffusion parameter by applying the Einstein relation. The simulation results indicated that increasing the temperature led to easing the migration of the molecules and decreasing the dependence of the movement of the molecules on each other. This growing trend of migration may lead to an increase in the self-diffusion coefficient of molecules. Structural analysis revealed that a ratio of 1:1 of glucose: choline chloride could provide the best condition to maintain the low melting point of the mixture due to the strong hydrogen-bonded network between the two species.