scholarly journals Characterization of Atomic Surface Roughness in Nanometric Machining Molecular Dynamics (MD) Simulations

2016 ◽  
Vol 13 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Akinjide Olufemi Oluwajobi ◽  
Xun Chen
Keyword(s):  
Molecular Dynamics ◽  
Surface Roughness ◽  
Md Simulations ◽  
Nanometric Machining ◽  
Atomic Surface

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.

scholarly journals Interface-governed nanometric machining behaviour of Cu/Ag bilayers using molecular dynamics simulation

RSC Advances ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 1341-1353 ◽  
Author(s):  
Qihong Fang ◽  
Yuanyuan Tian ◽  
Jia Li ◽  
Qiong Wang ◽  
Hong Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Cu Film ◽  
Nanometric Machining ◽  
Pure Cu

The nanometric machining of Cu/Ag bilayers and pure Cu film is performed using molecular dynamics (MD) simulations.

Molecular Dynamics Simulations of Thermal Conductivity of Bi2Te3 Nanowires

2009 ◽  
Author(s):  
Bo Qiu ◽  
Lin Sun ◽  
Xiulin Ruan
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Surface Roughness ◽  
Smooth Surface ◽  
Lattice Thermal Conductivity ◽  
Phonon Scattering ◽  
Md Simulations ◽  
Interatomic Potentials ◽  
Phonon Confinement ◽  
Dynamics Simulations

In this paper, by employing the previously developed two-body interatomic potentials for bismuth telluride, molecular dynamics (MD) simulations are used to describe the thermoelectric properties, namely the lattice thermal conductivity, of Bi2Te3 nanowires. Cylindrical nanowires with both smooth surface and sawtooth surface roughness are studied, aiming at revealing the effects of phonon confinement in 1-D structures, phonon boundary scatterings and surface roughness on the lattice thermal conductivity of Bi2Te3 nanowires. In the end, the influence of various phonon scattering mechanisms on the nanostructures under study are summarized, possible paths to reduce lattice thermal conductivity in nanostructured Bi2Te3, which is favorable for enhancing thermoelectric performance, are pointed out.

ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories

2020 ◽  
Vol 36 (11) ◽  
pp. 3576-3577 ◽  
Author(s):  
Marcelo D Polêto ◽  
Bruno I Grisci ◽  
Marcio Dorn ◽  
Hugo Verli
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Conformational Transition ◽  
Clustering Algorithms ◽  
Md Simulations ◽  
Conformational Space ◽  
Supplementary Information ◽  
Conformational Sampling ◽  
Conformational Population

Abstract Motivation The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts. Results Here, we introduce ConfID, an analytical tool for conformational characterization of small molecules using MD trajectories. The evolution of conformational sampling and population frequencies throughout trajectories is calculated to check for sampling convergence while allowing to map relevant conformational transitions. The tool is designed to track conformational transition events and calculate time-dependent properties for each conformational population detected. Availability and implementation Toolkit and documentation are freely available at http://sbcb.inf.ufrgs.br/confid Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Molecular Dynamics Simulation of Nanometric Machining Under Realistic Cutting Conditions

2008 ◽  
Author(s):  
R. Promyoo ◽  
H. El-Mounayri ◽  
X. Yang
Keyword(s):  
Molecular Dynamics ◽  
Cutting Force ◽  
Chip Formation ◽  
Thrust Force ◽  
Cutting Speed ◽  
Md Simulations ◽  
Rake Angle ◽  
Dynamics Simulation ◽  
Depth Of Cut ◽  
Nanometric Machining

Molecular Dynamics (MD) simulations of nanometric machining of single-crystal copper were conducted at a conventional cutting speed (5m/s) and different depths of cut (0.724 – 2.172 nm). The simulations were carried out to predict cutting forces and investigate the mechanism of chip formation at the nano level. The effect of tool rake angles and depths of cut on the mechanism of chip formation were also investigated. Tools with different rake angles, namely 0°, 5°, 10°, 15°, 30°, and 45°, were used. It was found that the cutting force, thrust force, and the ratio of the thrust force to cutting force decrease with increasing rake angle. However, the ratio of the thrust force to the cutting force is found to be independent of the depth of cut.

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.

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

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.

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