A molecular dynamics study: Structures and thermal stability of PdmPt(13−m)Ag42 ternary nanoalloys

2018 ◽  
Vol 29 (09) ◽  
pp. 1850084 ◽  
Author(s):  
Ali Kemal Garip
Keyword(s):  
Molecular Dynamics ◽  
Cohesive Energy ◽  
Canonical Ensemble ◽  
Interatomic Interaction ◽  
Md Simulations ◽  
Many Body ◽  
Melting Temperatures ◽  
Body Potential ◽  
Basin Hopping ◽  
Thermal Stability Of

Structural optimization of ternary PdmPt[Formula: see text]Ag[Formula: see text] nanoalloys was performed using the basin-hopping algorithm, and the Gupta many-body potential was adopted to model interatomic interaction. The optimization results show that all compositions have a structure based on icosahedron with a core–shell segregation. While the Ag atoms prefer to segregate to the surface, Pd and Pt atoms were located at the core of the cluster due to the higher surface and cohesive energy. The single platinum atom with the highest cohesive energy in Pd[Formula: see text]Pt1Ag[Formula: see text] nanoalloy was located at the center of the cluster. Also in all other compositions except Pd[Formula: see text]Ag[Formula: see text], Pd atoms occupy the second shell position of the icosahedron structure. We used classical molecular dynamics (MD) simulations in canonical ensemble conditions (NVT) to investigate the melting temperatures of ternary PdmPt[Formula: see text]Ag[Formula: see text] nanoalloys with the interatomic interactions modeled by the same potential with optimizations. The icosahedral structures were taken as the initial configurations for MD simulations. We obtained caloric curves and Lindemann indexes to investigate the melting transitions. The simulation results showed that varying the composition gives rise to a fluctuation in melting temperatures. The highest melting temperature belongs to the Pd9Pt4Ag[Formula: see text] nanoalloy cluster within the other compositions. However, the relative stability investigation indicates the Pd8Pt5Ag[Formula: see text] nanoalloy cluster as the most stable composition. The Lindemann indexes obtained for the second and third shell of icosahedral structures show that the melting takes place as a whole without any surface premelting.

Size and composition effect on structural properties and melting behaviors of Cu–Ag–Au ternary nanoalloys

2020 ◽  
Vol 31 (06) ◽  
pp. 2050078
Author(s):  
Huseyin Yildirim ◽  
Haydar Arslan
Keyword(s):  
Mean Square Displacement ◽  
Melting Process ◽  
Md Simulations ◽  
Composition Effect ◽  
Many Body ◽  
Melting Temperatures ◽  
The Core ◽  
Dynamical Behaviors ◽  
Body Potential ◽  
Basin Hopping

Structural optimization of ternary Cu–Ag–Au nanoalloys with 38 and 55 atoms was performed using the basin-hopping algorithm and the Gupta many-body potential was adopted to model interatomic interactions. The optimization results show that, while the Ag atoms prefer to segregate to the surface, Cu atoms were located at the core of the nanoalloy due to the higher surface and cohesive energy, whereas Au atoms mainly are located on the surface of the nanoalloys. It is found that the size has little effect on the segregation phenomena of Cu, Ag and Au atoms in the Cu–Ag–Au ternary nanoalloy. We estimated the melting temperatures of Cu–Ag–Au ternary nanoalloys using caloric curves and Lindemann index data obtained from classical molecular dynamics (MD) simulations. The results showed that the melting temperature is closely associated with the size and composition of the nanoalloys and varying the composition gives rise to a fluctuation in melting temperatures. Also, structural evolutions and dynamical behaviors of nanoalloys in melting process are investigated with root mean square displacement (RMSD).

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

Simulation of Thermal Stability and Friction: A Lubricant Confined Between Monolayers of Wear Inhibitors on Iron Oxide

1998 ◽  
Vol 543 ◽  
Author(s):  
T. Çağin ◽  
Y. Zhou ◽  
E. S. Yamaguchi ◽  
R. Frazier ◽  
A. Ho ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Quantum Chemical ◽  
Md Simulations ◽  
Atomic Level ◽  
The Self ◽  
Self Assembled Monolayer ◽  
Thermal Stabilities ◽  
Frictional Forces ◽  
Thermal Stability Of

AbstractTo understand antiwear phenomena in motor engines at the atomic level and provide evidence inselecting future ashless wear inhibitors, we studied the thermal stability of the self-assembled monolayer(SAM) model for dithiophosphate (DTP) and dithiocarbamate (DTC) molecules on the iron oxidesurface using molecular dynamics. The interactions for DTP, DTC and Fe2O3 are evaluated based on aforce field derived from fitting to ab initio quantum chemical calculations of dimethyl DTP (and DTC)and Fe(OH)2(H2O)2-DTP (DTC) clusters. MD simulations at constant-NPT are conducted to assesrelative thermal stabilities of the DTP and DTC with different pendant groups (n-propyl, i-propyl, npentyl.and i-pentyl). To investigate frictional process, we employ a steady state MD method, in whichone of the Fe2O3 slabs maintained at a constant linear velocity. We obtain the time averaged normaland frictional forces from the interatomic forces. Then, we calculated the friction coefficient at theinterface between SAMs of DTP and the confined lubricant, hexadecane, to assess the shear stability ofDTPs with different pendant groups.

scholarly journals A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

2021 ◽  
Vol 22 (19) ◽  
pp. 10813
Author(s):  
Congcong Li ◽  
Zhongkui Lu ◽  
Min Wang ◽  
Siao Chen ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Graphene Oxide ◽  
Md Simulations ◽  
Strong Interactions ◽  
Limiting Factor ◽  
Active Site Residues ◽  
Detailed Mechanism ◽  
Dynamics Simulations ◽  
Thermal Stability Of

Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

GLOBAL MINIMA FOR PdN (N = 5–80) CLUSTERS DESCRIBED BY SUTTON–CHEN POTENTIAL

2007 ◽  
Vol 18 (08) ◽  
pp. 1351-1359 ◽  
Author(s):  
HAYDAR ARSLAN
Keyword(s):  
Monte Carlo ◽  
Energy Surface ◽  
Central Atom ◽  
Low Energy ◽  
Global Minima ◽  
Many Body ◽  
Pd Clusters ◽  
Body Potential ◽  
Basin Hopping ◽  
Theoretical Results

The structure and energetics of Pd N (N = 5–80) clusters have been studied extensively by a Monte Carlo method based on Sutton–Chen many-body potential. The basin-hopping algorithm is used to find the low-energy minima on the potential energy surface for each nuclearity. A variety of structure types (icosahedral, decahedral and fcc closed-packed) are observed for Pd clusters. Some of the icosahedral global minima do not have a central atom. The resulting structures have been compared with the previous theoretical results.

EFFECT OF CHIRALITY ON THE STABILITY OF CARBON NANOTUBES: MOLECULAR-DYNAMICS SIMULATIONS

2001 ◽  
Vol 12 (06) ◽  
pp. 865-870 ◽  
Author(s):  
ŞAKIR ERKOÇ ◽  
OSMAN BARIŞ MALCIOĞLU
Keyword(s):  
Heat Treatment ◽  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Potential Energy Function ◽  
Single Wall Carbon Nanotubes ◽  
Many Body ◽  
Chiral Structure ◽  
The Stability ◽  
Dynamics Simulations ◽  
Body Potential

The effect of chirality on the structural stability of single-wall carbon nanotubes have been investigated by performing molecular-dynamics computer simulations. Calculations have been realized by using an empirical many-body potential energy function for carbon. It has been found that carbon nanotube in chiral structure is more stable under heat treatment relative to zigzag and armchair models. The diameter of the tubes is slightly enlarged under heat treatment.

Thermal stability of marks gold nanoparticles: A molecular dynamics simulation

2017 ◽  
Vol 31 (07) ◽  
pp. 1741001
Author(s):  
Yanlin Jia ◽  
Siqi Li ◽  
Weihong Qi ◽  
Mingpu Wang ◽  
Zhou Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Melting Temperature ◽  
Cohesive Energy ◽  
Au Nanoparticles ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Structure Variation ◽  
Deformation Parameters ◽  
Thermal Stability Of

Molecular dynamics (MDs) simulations were used to explore the thermal stability of Au nanoparticles (NPs) with decahedral, cuboctahedral, icosahedral and Marks NPs. According to the calculated cohesive energy and melting temperature, the Marks NPs have a higher cohesive energy and melting temperature compared to these other shapes. The Lindemann index, radial distribution function, deformation parameters, mean square displacement and self-diffusivity have been used to characterize the structure variation during heating. This work may inspire researchers to prepare Marks NPs and apply them in different fields.

Molecular Dynamics Simulations of Atoms Diffusion in Solid

2018 ◽  
Vol 15 ◽  
pp. 51-64
Author(s):  
Yu Lu Zhou ◽  
Xiao Ma Tao ◽  
Qing Hou ◽  
Yi Fang Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Einstein Relation ◽  
Interatomic Potentials ◽  
Body System ◽  
Many Body ◽  
Point Particles ◽  
Bulk Surface ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations, which treat atoms as point particles and trace their individual trajectories, are always employed to investigate the transport properties of a many-body system. The diffusion coefficients of atoms in solid can be obtained by the Einstein relation and the Green-Kubo relation. An overview of the MD simulations of atoms diffusion in the bulk, surface and grain boundary is provided. We also give an example of the diffusion of helium in tungsten to illustrate the procedure, as well as the importance of the choice of interatomic potentials. MD simulations can provide intuitive insights into the atomic mechanisms of diffusion.

Effect of Size on the Mechanical Properties of Rh-20at%Pd Nanowire

2011 ◽  
Vol 403-408 ◽  
pp. 1173-1177
Author(s):  
Jamal Davoodi ◽  
Mohammad Javad Moradi
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Bulk Modulus ◽  
Elastic Constants ◽  
Constant Pressure ◽  
Young Modulus ◽  
Dynamics Simulation ◽  
Many Body ◽  
Temperature Constant ◽  
Body Potential

The aim of this research was to calculate Yong modulus, Bulk modulus and the elastic constants of Rh-20at%Pd (atom percent) nanowire. The molecular dynamics simulation technique was used to calculate the mechanical properties at constant temperature, constant pressure ensemble. The cohesive energy of the model nanowire systems was calculated by Quantum Sutton-Chen many body potential. The temperature and the pressure of the system were controlled by Nose-Hoover thermostat and Berendsen barostat, respectivly. In addition effects of the diameter of nanowire on the mechanical properties were studied. The obtained results show that, when the diameter of Rh-Pd nanowire increase, elastic constants, bulk modulus and Young modulus all increase, and when the diameter reaches about 5.5 nm, the properties began to level off and remain constant.

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