Influence of initial distance and heating rate on the aggregation of Cu and Au nanoparticles: a MD study

This paper investigates the effects of interparticle distance and heating rate on the aggregation characteristics of Cu/Au nanoparticles using molecular dynamics (MD) simulations, and focuses on discussing the effects of the two above-mentioned factors on the entire system. Our results suggested that the reduction in heating rate and increasing the initial distance of the particles would both contribute to raising the initial sintering temperature. However, when the particles’ initial distance was greater than the cut-off radius of the system, the initial sintering temperature was not increased any longer, but fluctuated within a certain range. Furthermore, the sintering force of the nanoparticles at the initial sintering temperature was investigated, and it was found that the heating rate made no obvious difference to it. Nonetheless, the sintering force varied under different initial distance of the particles (at the same heating rate) due to system energy changes.

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Study on Nanoimprint Lithography of the Polymer Chains (CH2)n With Anti-Adhesion Layer on Stamp by Molecular Dynamics Method

ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels ◽

10.1115/icnmm2008-62172 ◽

2008 ◽

Author(s):

Quang-Cherng Hsu ◽

Chien-Liang Lin ◽

Te-Hua Fang

Keyword(s):

Molecular Dynamics ◽

Polymer Material ◽

Nanoimprint Lithography ◽

Minimum Energy ◽

Md Simulations ◽

Atomic Scale ◽

Polymer Materials ◽

Energy Status ◽

Adhesion Layer ◽

System Energy

This paper aims at the study on nanoimprint lithography (NIL) of the polymer material in (CH2)n Chains. The simulation codes were built based on molecular dynamics (MD) method for observing material deformation behaviors in atomic scale. The deformation mechanism of NIL of polymer material (CH2)n pressed by silicon stamp was first studied, by which the effects of critical punch tip width, imprint depth, temperature, and adhesion effect were studied. Next, the nanoimprint processes with stamp tips covered by anti-adhesion material, which is a self-assembled monolayer (SAM), were studied to compare to those processes without having anti-adhesion layer. When deforming polymer material at or above room temperature, adhesion problems occur between stamp and polymer. Polymer materials adhere to stamp more severe than they adhere to each others because potential energies between long chains of polymers are smaller than those between polymer and stamp. From the relation between system energy and stamp translation based on the MD simulations, the system energy increases when stamp moves gradually. When unloading, the system energy will return to its minimum energy status and remains stable. However, when punch leaves polymer materials, energy fluctuation occurs due to some polymer materials adhere to the stamp. Finally, the analysis of stamp with and without SAM based on the MD method was conducted and discussed.

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Molecular Dynamics Simulation of the Cu/Au Nanoparticle Alloying Process

Journal of Nanomaterials ◽

10.1155/2019/7612805 ◽

2019 ◽

Vol 2019 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Linxing Zhang ◽

Qibin Li ◽

Sen Tian ◽

Guang Hong

Keyword(s):

Molecular Dynamics ◽

Material Properties ◽

Au Nanoparticles ◽

Sintering Temperature ◽

Dynamics Simulation ◽

Au Nanoparticle ◽

Thermodynamic Process ◽

Important Approach ◽

Molecular Dynamics Methods ◽

Sintering Neck

Sintering is an important approach for the alloying of different metals, which is affected by factors such as temperature, grain size, and material properties. And it represents a complex thermodynamic process. This paper had adopted the molecular dynamics methods to investigate the evolution process of nanostructure during the sintering of Cu and Au nanoparticles. The changes in crystalline during the nanosintering process were observed, and the radial distribution function of atoms, the shrinkage ratio, and the sintering neck of the systems were discussed. The initial sintering temperature and melting temperature of the system were obtained; at the same time, the characteristics of the sintering neck with changes in temperature during the nanosintering process were revealed.

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Efficient Treatment of Fixed and Induced Dipolar Interactions

MRS Proceedings ◽

10.1557/proc-653-z7.22 ◽

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.

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

10.26434/chemrxiv.9783155.v2 ◽

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

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.

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

Letters in Drug Design & Discovery ◽

10.2174/1570180815666180604085626 ◽

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). 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. 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. 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.

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Optimization of Sintering Process of Alumina Ceramics Using Response Surface Methodology

Sustainability ◽

10.3390/su13126739 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6739

Author(s):

Darko Landek ◽

Lidija Ćurković ◽

Ivana Gabelica ◽

Mihone Kerolli Mustafa ◽

Irena Žmak

Keyword(s):

Response Surface Methodology ◽

Response Surface ◽

Heating Rate ◽

Sintering Temperature ◽

Nonlinear Models ◽

Slip Casting ◽

Holding Time ◽

Alumina Ceramics ◽

Aqueous Suspensions ◽

Temperature Heating

In this work, alumina (Al2O3) ceramics were prepared using an environmentally friendly slip casting method. To this end, highly concentrated (70 wt.%) aqueous suspensions of alumina (Al2O3) were prepared with different amounts of the ammonium salt of a polycarboxylic acid, Dolapix CE 64, as an electrosteric dispersant. The stability of highly concentrated Al2O3 aqueous suspensions was monitored by viscosity measurements. Green bodies (ceramics before sintering) were obtained by pouring the stable Al2O3 aqueous suspensions into dry porous plaster molds. The obtained Al2O3 ceramic green bodies were sintered in the electric furnace. Analysis of the effect of three sintering parameters (sintering temperature, heating rate and holding time) on the density of alumina ceramics was performed using the response surface methodology (RSM), based on experimental data obtained according to Box–Behnken experimental design, using the software Design-Expert. From the statistical analysis, linear and nonlinear models with added first-order interaction were developed for prediction and optimization of density-dependent variables: sintering temperature, heating rate and holding time.

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

Polymers ◽

10.3390/polym13010099 ◽

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

Molecules ◽

10.3390/molecules26061711 ◽

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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Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽

10.1039/d0ce01613f ◽

2021 ◽

Author(s):

Andrey Sarikov ◽

Anna Marzegalli ◽

Luca Barbisan ◽

Massimo Zimbone ◽

Corrado Bongiorno ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Stacking Faults ◽

Md Simulations ◽

Stacking Fault ◽

Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

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

Sensors ◽

10.3390/s21082621 ◽

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.

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