scholarly journals Molecular Dynamics Study on Structural and Atomic Evolution Between Au and Ni Nanoparticles Through Coalescence

2021 ◽  
Author(s):  
Bangquan Li ◽  
Jing Li ◽  
Xiaoqiang Su ◽  
Yimin Cui
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Thermal Control ◽  
Structure Evolution ◽  
Continuous Heating ◽  
Heating Process ◽  
Au Nps ◽  
Atomic Segregation ◽  
Spherical Structures ◽  
Increasing Temperature

Abstract Motivated by the structure evolution experiments of Janus NiAu nanoparticles (NPs), we present a detailed study on the thermodynamic evolution of Ni and Au NPs with different ratios of Au and Ni through the molecular dynamics (MD) simulations. It is found that, for fixed Ni particle size (5.8 nm in diameter), the energy variation with the increasing temperature is related to the Au sizes (1.5–9.6 nm in diameter), due to the diverse atomic segregation modes. For a small Au particle, due to lattice induction, the structure will change from order to disorder and then to order. The interface defects of the merging NPs could be automatically eliminated by coalescence processes. The change in energy as the temperature increases is similar to that of monometallic NPs. For larger Au particles, the irregular variation of energy occurs and the atomic energy experience one or two reductions with the increase of the temperature. The segregation of Au atoms to the surface of Ni particle is dominant during the continuous heating process. The coalescence processes of Au atoms strongly determine the final morphology of the particles. Dumbbell-like, Janus and eccentric core-shell spherical structures could be obtained during the heating process. Our results will provide an effective approach to the design of novel materials with specific properties through thermal control.

scholarly journals Molecular dynamics study on structural and atomic evolution between Au and Ni nanoparticles through coalescence

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bangquan Li ◽  
Jing Li ◽  
Xiaoqiang Su ◽  
Yimin Cui
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Thermal Control ◽  
Structure Evolution ◽  
Continuous Heating ◽  
Heating Process ◽  
Au Nps ◽  
Atomic Segregation ◽  
Spherical Structures ◽  
Increasing Temperature

AbstractMotivated by the structure evolution experiments of Janus NiAu nanoparticles (NPs), we present a detailed study on the thermodynamic evolution of Ni and Au NPs with different ratios of Au and Ni through the molecular dynamics (MD) simulations. It is found that, for fixed Ni particle size (5.8 nm in diameter), the energy variation with the increasing temperature is related to the Au sizes (1.5–9.6 nm in diameter), due to the diverse atomic segregation modes. For a small Au particle, due to lattice induction, the structure will change from order to disorder and then to order. The interface defects of the merging NPs could be automatically eliminated by coalescence processes. The change in energy as the temperature increases is similar to that of monometallic NPs. For larger Au particles, the irregular variation of energy occurs and the atomic energy experience one or two reductions at least with the increase of the temperature. The segregation of Au atoms to the surface of Ni particle is dominant during the continuous heating process. The coalescence processes of Au atoms strongly determine the final morphology of the particles. Dumbbell-like, Janus and eccentric core–shell spherical structures could be obtained during the heating process. Our results will provide an effective approach to the design of novel materials with specific properties through thermal control.

Competition between stability of icosahedral and cuboctahedral morphologies in bimetallic nanoalloys

2017 ◽  
Vol 19 (22) ◽  
pp. 14659-14670 ◽  
Author(s):  
Hamed Akbarzadeh ◽  
Mohsen Abbaspour ◽  
Esmat Mehrjouei
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Heating Process ◽  
Core Shell

In this study, we investigated the heating process for pure (Rh55 and Cu55), single dopant (Rh1Cu54 and Rh54Cu), core@shell (Rh13@Cu42 and Cu13@Rh42), and alloy (Rh13Cu42, Rh42Cu13) nanoclusters in two structures (cuboctahedral and icosahedral) from 0 to 2000 K using molecular dynamics (MD) simulations.

MOLECULAR DYNAMICS SIMULATION STUDY OF ATOMIC SEGREGATION OF (PdPt)147 DURING THE HEATING PROCESS

2012 ◽  
Vol 26 (08) ◽  
pp. 1250051 ◽  
Author(s):  
X. Y. XIAO ◽  
Z. F. CHENG ◽  
J. H. XIA
Keyword(s):  
Molecular Dynamics ◽  
Melting Process ◽  
Dynamics Simulation ◽  
Heating Process ◽  
Embedded Atom Method ◽  
Bimetallic Cluster ◽  
Embedded Atom ◽  
Atomic Segregation ◽  
Segregation Process ◽  
Alloy Concentration

Research on the influence of alloy concentration and distribution on bimetallic cluster plays a key role in exploring new structural material. This paper studies the melting process of icosahedral bimetallic cluster (PdPt)147 with different Pt concentrations and different atomic distributions by using molecular dynamics with an embedded atom method. The results indicate that the mixed Pd–Pt cluster shows an irregular phenomenon between 580 and 630 K, i.e. the atomic energy decreases with the increase of temperature. This is because the surface energy of Pd is lower than that of Pt; the decreased energy due to Pd atomic segregation is larger than the increased energy due to heating during the segregation process. In addition, the temperature of Pd atomic segregation is strongly related to Pt concentration. This leads to that Pd atoms prefer to remain on the surface even after the cluster melted.

scholarly journals Molecular Dynamics Simulation on Structure and Dielectric Permittivity of BaTiO3/PVDF Composites

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Ruitian Bo ◽  
Junwang Liu ◽  
Chunfeng Wang ◽  
Yongliang Wang ◽  
Peigang He ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dielectric Permittivity ◽  
Vinylidene Fluoride ◽  
Volume Fraction ◽  
Morphological Structure ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Structure Evolution ◽  
Particle Model ◽  
Β Phase

Molecular dynamics (MD) simulation was performed to investigate the structure and dielectric permittivity of poly(vinylidene fluoride)- (PVDF-) based composites with different contents of barium titanate (BT). The β-phase PVDF model with 100 structural units and the spherical BT particle model with a radius of 0.495 nm were built and applied in the initial models with three PVDF macromolecular chains and BT particles for the MD simulations of the BT/PVDF composites. The influences of BT content on the morphological structure, the free volume fraction, and glass transition temperature of the composites were explored according to the simulated results and the experimental ones of X-ray diffraction (XRD) and scanning electron microscope (SEM). A model was proposed to predict the static dielectric permittivity of the composites, the results of which were compared with the Cole-Cole fitting results of dielectric spectroscopy. Attempts were made to reveal the structure evolution and the micropolarization mechanism with the increasing content of BT.

Density Functional Theory and Ab Initio Molecular Dynamics Study of the Effect of Ti and Zr Transition Metals in D03 Fe3Al

2012 ◽  
Vol 706-709 ◽  
pp. 1095-1099
Author(s):  
Sara Chentouf ◽  
Jean Marc Raulot ◽  
Hafid Aourag ◽  
Thierry Grosdidier
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Functional Theory ◽  
Ab Initio Md ◽  
Increasing Temperature ◽  
Formation Energies

The formation energies of the T.M impurities Ti and Zr were calculated using DFT calculations at absolute zero and ab initio MD simulations at 300 K. We found that, with increasing temperature, Zr impurities become more stable and prefer to segregate at the interface of ∑5 (310)[001] grain boundary. In the case of Ti, the results show that it remains a stable defect when temperature increases.

Study of Helium Bubble Induced Hardening in BCC-Fe by Molecular Dynamics Simulation

2019 ◽  
Vol 944 ◽  
pp. 378-386
Author(s):  
Li Xia Jia ◽  
Xin Fu He ◽  
Shi Wu ◽  
Dong Jie Wang ◽  
Han Cao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Edge Dislocation ◽  
Reasonable Agreement ◽  
Md Simulation ◽  
Md Simulations ◽  
Defect Size ◽  
Dynamics Simulation ◽  
Helium Bubble ◽  
Increasing Temperature ◽  
Critical Resolved Shear Stress

The interaction between an moving edge dislocation and helium bubble was studied in BCC-Fe using Molecular dynamics（MD）simulation. Edge dislocation passed the bubble via cut mechanism. A step with a length of b is left on both sides of the bubble after dislocation left away. The influence of simulation temperature, defect size and He/V ratio in bubble on critical resolved shear stress (CRSS) for dislocation to shear bubble were investigated. The CRSS increases with increasing defect sizes, and decreases with increasing temperature. When He/V ratio is at the range of 0-1, CRSS depends weakly on the He/V ratio. The estimated obstacle strength of helium bubble based on MD simulations is acceptable and reasonable agreement with one deduced from the dispersion barrier-hardening model applied to experimental results.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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