SIMULATION OF ENERGETIC CLUSTER IMPACTS ON METALLIC TARGETS

1991 ◽  
Vol 05 (05) ◽  
pp. 341-349 ◽  
Author(s):  
M.H. SHAPIRO ◽  
T.A. TOMBRELLO
Keyword(s):  
Molecular Dynamics ◽  
Recent Progress ◽  
Md Simulations ◽  
Cluster Ions ◽  
Confinement Time ◽  
Number Density ◽  
Metallic Surfaces ◽  
Energy Distributions ◽  
Highly Nonlinear

We review recent progress in the use of molecular dynamics (MD) simulations to study the energetic collisions of cluster ions with metallic surfaces. MD simulations have been used to predict the energy, number-density, and confinement-time properties of the highly nonlinear collision cascades initiated by cluster impacts; as well as to predict the yields, energy-distributions, and angle-distributions of ejected cluster-atoms and target-atoms.

Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol revisited

2004 ◽  
Vol 76 (1) ◽  
pp. 247-254 ◽  
Author(s):  
H. Torii
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Pressure Dependence ◽  
Md Simulations ◽  
Liquid Structure ◽  
Present Calculation ◽  
Number Density ◽  
Transition Dipole ◽  
Liquid Systems

Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol is examined with the combination of molecular dynamics (MD) simulations and the intermolecular resonant vibrational interactions determined by the transition dipole coupling (TDC) mechanism (MD/TDC method). It is shown that the observed decrease of the Raman noncoincidence νNCE of the CO stretching band with increasing density reported in the literature is quantitatively reproduced by the present calculation. As the density increases, the hydrogen bonds get slightly shorter, but molecules belonging to different hydrogen-bond chains get closer to each other to a greater extent. This anisotropic change in the liquid structure is the reason for the behavior of νNCE. It is also shown that the concentration dependence of νNCE in the methanol/CCl4 binary mixtures reported in a previous study, and the pressure dependence of νNCE in methanol may be described in a consistent way as a function of the number density of methanol in the liquid systems.

Molecular Dynamics Simulations of Cluster-size Effect on Sputtering Process with Reactive Gas Cluster Ions

2005 ◽  
Vol 908 ◽  
Author(s):  
Takaaki Aoki ◽  
Jiro Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Size Effect ◽  
Cluster Size ◽  
Incident Energy ◽  
Md Simulations ◽  
Cluster Ions ◽  
Experimental Conditions ◽  
Near Surface ◽  
The Impact ◽  
Reactive Cluster

AbstractTo investigate the size-effect of reactive clusters on sputtering processes, we performed molecular dynamics (MD) simulations of reactive cluster ions with various sizes impacting on solid targets. Various sizes of fluorine clusters, (F2)30, (F2)300 and (F2)3000, were irradiated on a Si(100) target at the same total incident energy of 6 keV. These clusters were irradiated on the same target one after another in order to reproduce real experimental conditions such as the accumulation of fluorine atoms in the target. The MD simulations of sequential cluster impacts enabled to perform various statistical analyses regarding the sputtered particles. The study of cluster size distributions showed that the sputtering process by reactive cluster ion impact has similarity with the emission from quasi-liquid materials excited to hyper-thermal conditions by ion bombardment. However, the major sputtered particles were different with each other; Si for (F2)30 (100 eV/atom), SiF2 for (F2)300 (10 eV/atom), and SiF3 for (F2)3000 (1 eV/atom). At the impact of a large size cluster with low incident energy, a large number of Si-F bondings were generated at the cluster-target interface surface, which enhances formation of volatile SiFx compounds with many fluorine atoms. In contrast, a small cluster with high kinetic energy-per-atom could cause the formation of numerous energetic surface atoms at the near surface region, which could be sputtered without being well fluoridated.

Recent Advances in the In-silico Structure-based and Ligand-based Approaches for the Design and Discovery of Agonists and Antagonists of A2A Adenosine Receptor

2019 ◽  
Vol 25 (7) ◽  
pp. 774-782 ◽  
Author(s):  
Nikhil Agrawal ◽  
Balakumar Chandrasekaran ◽  
Amal Al-Aboudi
Keyword(s):  
Molecular Dynamics ◽  
Membrane Protein ◽  
In Silico ◽  
Recent Progress ◽  
Md Simulations ◽  
Pharmacophore Modeling ◽  
A2a Adenosine Receptor ◽  
A2a Receptor ◽  
In Silico Studies ◽  
The Family

A2A receptor belongs to the family of GPCRs, which are the most abundant membrane protein family. Studies in the last few decades have shown the therapeutic applications of A2A receptor in various diseases. In the present mini-review, we have discussed the recent progress in the in-silico studies of the A2A receptor. Herein, we described the different structures of A2A receptor, the discovery of new agonists and antagonists using virtualscreening/ docking, pharmacophore modeling, and QSAR based pharmacophore modeling. We have also discussed various molecular dynamics (MD) simulations studies of A2A receptor in complex with ligands.

Molecular Dynamics Simulations of Cluster Ion Impact on Diamond Surface

2000 ◽  
Vol 650 ◽  
Author(s):  
Takaaki Aoki ◽  
Jiro Matsuo ◽  
Gikan Takaoka ◽  
Isao Yamada
Keyword(s):  
Molecular Dynamics ◽  
Cluster Size ◽  
Incident Energy ◽  
Md Simulations ◽  
Cluster Ions ◽  
Diamond Surface ◽  
Cluster Ion ◽  
Sputtering Yield ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics (MD) simulations of various cluster ions impacting on solid targets were performed in order to examine the implant and damage formation processes. Ne and Ar rare gas cluster with various cluster sizes, and fullerene (C60) were impacted on diamond (001) surface. It was shown that the impact process of cluster ion depends on the cluster size. When the cluster size is small and incident energy-per-atom is high, such as Ar15 with 800eV/atom, all incident Ar atoms penetrate the surface and reside in the substrate. As the cluster size increases and the incident energy-per-atom decreases, the implant depth decreases and the profile of the displacement becomes shallower. A large cluster, such as Ar60 with 200eV/atom, shows a shallower implant depth and a higher sputtering yield than Ar15. However, Ar240 with 50eV/atom shows a shallower implant depth, but less sputtering yield than Ar60.These results suggest that there is proper cluster size and incident energy where the maximum sputtering yield is achieved.

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.

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

CrystEngComm ◽  
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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