Molecular Dynamics Simulation of the Alpha-Recoil Nucleus Displacement Cascade in Zirconolite

2001 ◽  
Author(s):  
L. Veiller ◽  
JP. Crocombette ◽  
C. Meis ◽  
D. Ghaleb
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Md Simulations ◽  
Recoil Nucleus ◽  
Dynamics Simulation ◽  
Α Decay ◽  
Cell Parameters ◽  
Displacement Cascades ◽  
Pair Potentials ◽  
High Level

Abstract Zirconolite (CaZrTi2O7) has been proposed as a crystalline ceramic host for the long-term disposal of actinides extracted from high-level nuclear waste (e.g. France) and from excess weapons-grade plutonium (e.g. USA). The disintegration of radionuclides induces modifications of the crystalline structure. During α-decay of actinides, localized cascades of displaced atoms occur primarily because of ballistic collisions in the material from the emitted α-recoil nuclei. Under α-decay irradiation, zirconolite undergoes a crystalline to amorphous transformation, which is associated to a volume expansion. We have focused our study on the understanding of radiation-induced structural changes at the atomic level in this ceramic. Molecular Dynamics (MD) has been used in the simulation of displacement cascades in zirconolite. Original Buckingham pair potentials have been established for zirconolite to characterize the two body short-range interactions between different ionic pairs. We present the potential parameters fitted to the structural equilibrium properties of the crystal. This fitting reproduces the characteristics of the cell parameters of zirconolite within 4% and gives reasonable values for the bulk modulus and the specific heat. The MD method is applied to determine the threshold displacement energies for the various sublattices. Finally, we have modelled the effects of displacement cascades in zirconolite, due to the α-recoil nuclei. For that purpose, two MD simulations of high recoil kinetic energies (2 and 6 keV) were performed. The preliminary results show that the complex matrix zirconolite tends to a structural disordering for high PKA energy values although a partial recrystallization step is observed during the energy dissipation.

Molecular-Dynamics Simulation of Displacement Cascades in Zircon (ZrSiO4)

1997 ◽  
Vol 506 ◽  
Author(s):  
J-P. Crocombette ◽  
D. Ghaleb
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Recoil Nucleus ◽  
Point Of View ◽  
Nuclear Industry ◽  
Dynamics Simulation ◽  
Α Decay ◽  
Displacement Cascades ◽  
Displacement Cascade ◽  
Amorphous Zone

ABSTRACTZircon (ZrSiO4) is of great interest for the nuclear industry as it is one of the new crystalline waste form considered for the disposal of actinides, for example weapons' plutonium in USA. In this study the effects of displacement cascade due to α-decay has been modelled from an atomistic point of view by molecular dynamics simulation using Born-Mayer-Huggins empirical potential. The numerical values of the parameters of this potential have been fitted on structural equilibrium properties of the crystal and on atomic arrangements.Displacement cascades are reproduced by accelerating one of the atoms of the cell, thus modelling the effect of the α-decay recoil nucleus. Kinetic energies up to 2 keV have been introduced. The unfolding of the cascades and the final structures have been studied in detail. The centre of the displacement cascade exhibits an amorphous zone where the zircon structure is completely lost. It contains an assembly of distorted SiO4 tetrahedra and disordered zirconium polyhedra. The zirconium ions (originally surrounded by 8 oxygen atoms) exhibit a decrease in their coordination number to 7 or 6 in agreement with what is observed for zirconium ions in amorphous zircon, zirconia or glasses. The size of the amorphous zone and the number of atoms displaced have been estimated for different recoil energies.The energy stored during the cascade has been calculated. It exhibits an overall good agreement with the available experimental data at complete amorphization.The existence of an amorphous track in our calculated cascades shows that the correct model for the amorphisation process should take into account the existence of a direct impact amorphous zone.

Choosing Appropriate Interatomic Potentials for Nanometric Molecular Dynamics (MD) Simulations

2016 ◽  
Vol 686 ◽  
pp. 194-199
Author(s):  
Akinjide O. Oluwajobi ◽  
Xun Chen
Keyword(s):  
Molecular Dynamics ◽  
Diamond Tool ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Embedded Atom ◽  
Pair Potentials ◽  
Empirical Potentials ◽  
Nanometric Machining ◽  
Cutting Processes

There is a need to choose appropriate interatomic empirical potentials for the molecular dynamics (MD) simulation of nanomachining, so as to represent chip formation and other cutting processes reliably. Popularly applied potentials namely; Lennard-Jones (LJ), Morse, Embedded Atom Method (EAM) and Tersoff were employed in the molecular dynamics simulation of nanometric machining of copper workpiece with diamond tool. The EAM potentials were used for the modelling of the copper-copper atom interactions. The pairs of EAM-Morse and EAM-LJ were used for the workpiece-tool (copper-diamond) atomic interface. The Tersoff potential was used for the carbon-carbon interactions in the diamond tool. Multi-pass simulations were carried out and it was observed that the EAM-LJ and the EAM-Morse pair potentials with the tool modelled as deformable with Tersoff potential were best suitable for the simulation. The former exhibit the lowest cutting forces and the latter has the lowest potential energy.

Molecular Dynamics Simulation of Recoil Nucleus Displacement Cascade in Zircon

1998 ◽  
Vol 540 ◽  
Author(s):  
Jean-Paul Crocombette ◽  
Dominique Ghaleb
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Simulations ◽  
Recoil Nucleus ◽  
Dynamics Simulation ◽  
Local Temperature ◽  
Displacement Cascades ◽  
Displacement Cascade ◽  
Temperature And Pressure

AbstractThe results of molecular simulations of a-recoil nucleus displacement cascades in zircon (ZrSiO4) are presented. The local temperature and pressure are found to increase dramatically during the cascade. The structure of the cascade tracks is amorphous. Its shape has been analyzed in terms of disordered and distorted cations. SiO2 nanophase are found to exist in the tracks consistently with what is observed in the experiments.

scholarly journals An Overview of Molecular Dynamics Simulation for Food Products and Processes

Processes ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 119
Author(s):  
Andrea Smith ◽  
Xin Dong ◽  
Vijaya Raghavan
Keyword(s):  
Molecular Dynamics ◽  
Food Processing ◽  
Structural Changes ◽  
Food Product ◽  
Food Products ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Chicken Breast ◽  
Optimal Processing ◽  
History Of

Molecular dynamics (MD) simulation is a particularly useful technique in food processing. Normally, food processing techniques can be optimized to favor the creation of higher-quality, safer, more functional, and more nutritionally valuable food products. Modeling food processes through the application of MD simulations, namely, the Groningen Machine for Chemical Simulations (GROMACS) software package, is helpful in achieving a better understanding of the structural changes occurring at the molecular level to the biomolecules present in food products during processing. MD simulations can be applied to define the optimal processing conditions required for a given food product to achieve a desired function or state. This review presents the development history of MD simulations, provides an in-depth explanation of the concept and mechanisms employed through the running of a GROMACS simulation, and outlines certain recent applications of GROMACS MD simulations in the food industry for the modeling of proteins in food products, including peanuts, hazelnuts, cow’s milk, soybeans, egg whites, PSE chicken breast, and kiwifruit.

scholarly journals Molecular Dynamics Simulation on the Interaction between Palygorskite Coating and Linear Chain Alkane Base Lubricant

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 286
Author(s):  
Jin Zhang ◽  
Lv Yang ◽  
Yue Wang ◽  
Huaichao Wu ◽  
Jiabin Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Molecular Diffusion ◽  
Linear Chain ◽  
Interfacial Interaction ◽  
Dynamics Simulation ◽  
Electrostatic Energy ◽  
Experimental Development ◽  
Practical Applications ◽  
Self Diffusion

Molecular dynamics (MD) simulations were conducted to investigate the interactions between a palygorskite coating and linear chain alkanes (dodecane C12, tetradecane C14, hexadecane C16, and octadecane C18), representing base oils in this study. The simulation models were built by placing the alkane molecules on the surface of the palygorskite coating. These systems were annealed and geometrically optimized to obtain the corresponding stable configurations, followed by the analysis of the structural changes occurring during the MD process. The interfacial interaction energies, mean square displacements, and self-diffusion coefficients of the systems were evaluated to characterize the interactions between base lubricant molecules and palygorskite coating. It was found that the alkanes exhibited self-arrangement ability after equilibrium. The interfacial interaction was attractive, and the electrostatic energy was the main component of the binding energy. The chain length of the linear alkanes had a significant impact on the intensity of the interfacial interactions and the molecular diffusion behavior. Moreover, the C12 molecule exhibited higher self-diffusion coefficient values than C14, C16 and C18. Therefore, it could be the best candidate to form an orderliness and stable lubricant film on the surface of the palygorskite coating. The present work provides new insight into the optimization of the structure and composition of coatings and lubricants, which will guide the experimental development of these systems for practical applications.

scholarly journals Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2621
Author(s):  
Seunghwa Yang
Keyword(s):  
Molecular Dynamics ◽  
Load Transfer ◽  
Cell Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Covalent Grafting ◽  
Modelling Strategies ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

Molecular Dynamics Simulation of the Displacement Cascades in Tungsten with Interstitial Helium Atoms

2014 ◽  
Vol 66 (1) ◽  
pp. 112-117 ◽  
Author(s):  
Xiaodan Yang ◽  
Huiqiu Deng ◽  
Nengwen Hu ◽  
Shifang Xiao ◽  
Cuilan Ren ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Helium Atoms ◽  
Displacement Cascades

A Study on the Uniaxial Tension of FCC Metals at Nano Level Using MD

2008 ◽  
Vol 32 ◽  
pp. 255-258
Author(s):  
Bohayra Mortazavi ◽  
Akbar Afaghi Khatibi
Keyword(s):  
Molecular Dynamics ◽  
Uniaxial Tension ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Face Centered Cubic ◽  
Engineering Strain ◽  
Fcc Metals ◽  
Engineering Stress ◽  
Nano Science ◽  
Face Centered

Molecular Dynamics (MD) are now having orthodox means for simulation of matter in nano-scale. It can be regarded as an accurate alternative for experimental work in nano-science. In this paper, Molecular Dynamics simulation of uniaxial tension of some face centered cubic (FCC) metals (namely Au, Ag, Cu and Ni) at nano-level have been carried out. Sutton-Chen potential functions and velocity Verlet formulation of Noise-Hoover dynamic as well as periodic boundary conditions were applied. MD simulations at different loading rates and temperatures were conducted, and it was concluded that by increasing the temperature, maximum engineering stress decreases while engineering strain at failure is increasing. On the other hand, by increasing the loading rate both maximum engineering stress and strain at failure are increasing.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

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