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 of the local concentration and structure in multicomponent aerosol nanoparticles under atmospheric conditions

2017 ◽  
Vol 19 (25) ◽  
pp. 16681-16692 ◽  
Author(s):  
Katerina S. Karadima ◽  
Vlasis G. Mavrantzas ◽  
Spyros N. Pandis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Organic Compound ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Core Shell ◽  
Local Concentration ◽  
Atmospheric Conditions ◽  
Aerosol Nanoparticles

MD simulations predicted core–shell or partially engulfed morphologies (depending on the type of the organic compound present) in multicomponent aerosol nanoparticles.

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.

scholarly journals Surface, Interface, and Temperature Effects on the Phase Separation and Nanoparticle Self Assembly of Bi-Metallic Ni0.5Ag0.5: A Molecular Dynamics Study

Nanomaterials ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 1040 ◽  
Author(s):  
Ryan H. Allaire ◽  
Abhijeet Dhakane ◽  
Reece Emery ◽  
P. Ganesh ◽  
Philip D. Rack ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Phase Diagram ◽  
Phase Separation ◽  
Self Assembly ◽  
Md Simulations ◽  
Bulk Sample ◽  
Immiscible Liquid ◽  
Core Shell ◽  
Shell Nanoparticles ◽  
Bimetallic Nanoparticle

Classical molecular dynamics (MD) simulations were used to investigate how free surfaces, as well as supporting substrates, affect phase separation in a NiAg alloy. Bulk samples, droplets, and droplets deposited on a graphene substrate were investigated at temperatures that spanned regions of interest in the bulk NiAg phase diagram, i.e., miscible and immiscible liquid, liquid-crystal, and crystal-crystal regions. Using MD simulations to cool down a bulk sample from 3000 K to 800 K, it was found that phase separation below 2400 K takes place in agreement with the phase diagram. When free surface effects were introduced, phase separation was accompanied by a core-shell transformation: spherical droplets created from the bulk samples became core-shell nanoparticles with a shell made mostly of Ag atoms and a core made of Ni atoms. When such droplets were deposited on a graphene substrate, the phase separation was accompanied by Ni layering at the graphene interface and Ag at the vacuum interface. Thus, it should be possible to create NiAg core-shell and layer-like nanostructures by quenching liquid NiAg samples on tailored substrates. Furthermore, interesting bimetallic nanoparticle morphologies might be tuned via control of the surface and interface energies and chemical instabilities of the system.

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.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

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