scholarly journals Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4

2021 ◽  
Vol 12 ◽  
pp. 1151-1172
Author(s):  
Alexey Prosvetov ◽  
Alexey V Verkhovtsev ◽  
Gennady Sushko ◽  
Andrey V Solov’yov
Keyword(s):  
Molecular Dynamics ◽  
Electron Beam ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Molecular Systems ◽  
Nanostructure Formation ◽  
Spatially Resolved ◽  
Software Packages ◽  
Precursor Molecules

This paper presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems by means of the advanced software packages MBN Explorer and MBN Studio. Atomistic simulations performed following the formulated protocol provide valuable insights into the fundamental mechanisms of electron-induced precursor fragmentation and the related mechanism of nanostructure formation and growth using FEBID, which are essential for the further advancement of FEBID-based nanofabrication. The developed computational methodology is general and applicable to different precursor molecules, substrate types, and irradiation regimes. The methodology can also be adjusted to simulate the nanostructure formation by other nanofabrication techniques using electron beams, such as direct electron beam lithography. In the present study, the methodology is applied to the IDMD simulation of the FEBID of Pt(PF3)4, a widely studied precursor molecule, on a SiO2 surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including the nucleation of Pt atoms and the formation of small metal clusters on the surface, followed by their aggregation and the formation of dendritic platinum nanostructures. The analysis of the simulation results provides spatially resolved relative metal content, height, and growth rate of the deposits, which represents valuable reference data for the experimental characterization of the nanostructures grown by FEBID.

scholarly journals A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

2021 ◽  
Author(s):  
Albert Smith ◽  
Alexander Vogel ◽  
Oskar Engberg ◽  
Peter Hildebrand ◽  
Daniel Huster
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membranes ◽  
Nmr Relaxation ◽  
Dynamics Simulation ◽  
Molecular Systems ◽  
Biological Interface ◽  
Novel Approach ◽  
Wide Range ◽  
Dynamic Landscape

Abstract Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report a novel approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use NMR relaxation and molecular dynamics simulation data for the characterization of lipid membranes, the most important biological interface. We develop a dynamics detector method that yields site-specific amplitudes, separated both by type and timescale of motion. This separation allows the detailed description of the dynamic landscape, which reveals vast differences in motion depending on molecular position. More generally, the method is applicable to a broad range of molecular systems, and can be adapted to other timescale-sensitive techniques.

scholarly journals A Web-Based Tool for Simulating Molecular Dynamics in Cloud Environments

Electronics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 185
Author(s):  
Gonzalo Nicolas-Barreales ◽  
Aaron Sujar ◽  
Alberto Sanchez
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Simulation ◽  
Cloud Environment ◽  
Web Based ◽  
Molecular Systems ◽  
Software Packages ◽  
Data Pipeline ◽  
Memory Power ◽  
Cloud Environments ◽  
Dynamics Simulations

Molecular dynamics simulations take advantage of supercomputing environments, e.g., to solve molecular systems composed of millions of atoms. Supercomputers are increasing their computing and memory power while they are becoming more complex with the introduction of Multi-GPU environments. Despite these capabilities, the molecular dynamics simulation is not an easy process. It requires properly preparing the simulation data and configuring the entire operation, e.g., installing and managing specific software packages to take advantage of the potential of Multi-GPU supercomputers. We propose a web-based tool that facilitates the management of molecular dynamics workflows to be used in combination with a multi-GPU cloud environment. The tool allows users to perform data pipeline and run the simulation in a cloud environment, even for those who are not specialized in the development of molecular dynamics simulators or cloud management.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

Molecular dynamics simulation study on characterization of bis(triethoxysilyl)-ethane and bis(triethoxysilyl)ethylene derived silica-based membranes

2013 ◽  
Vol 51 (25-27) ◽  
pp. 5248-5253 ◽  
Author(s):  
Takashi Shimoyama ◽  
Tomohisa Yoshioka ◽  
Hiroki Nagasawa ◽  
Masakoto Kanezashi ◽  
Toshinori Tsuru
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation

scholarly journals A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Albert A. Smith ◽  
Alexander Vogel ◽  
Oskar Engberg ◽  
Peter W. Hildebrand ◽  
Daniel Huster
Keyword(s):  
Molecular Dynamics ◽  
Nmr Relaxation ◽  
Dynamics Simulation ◽  
Comprehensive Description ◽  
Correlation Times ◽  
Wide Range ◽  
Dynamic Landscape ◽  
C Nmr ◽  
Analysis Of Motion

AbstractBiomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

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