Qualitative Study of Nanocluster Positioning Process: 2D Molecular Dynamics Simulations

2008 ◽  
Author(s):  
S. H. Mahboobi ◽  
A. Meghdari ◽  
N. Jalili ◽  
F. Amiri
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Interatomic Potential ◽  
Computation Time ◽  
Building Blocks ◽  
Manipulation System ◽  
Nanoscale Interactions ◽  
Particle Nature ◽  
Dynamics Simulations

One of the key factors in the assembly of nanoclusters is the precise positioning of them by a manipulation system. Currently the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in the manipulator/cluster/substrate interactions. Having a deeper insight to the aforementioned nanoscale interactions is crucial for prediction and understanding of the behavior of nanoclusters during the positioning process. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviors. Performing planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is greatly reduced in comparison to 3D simulations. The system consists of a tip, cluster and substrate. The focus of the present research is on ultra-fine metallic nanoclusters. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the above system which is made from different transition metals. The effects of material type, tip form and manipulation strategy on the success of the process have been investigated by planar molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming large-scale computation time or high experimental expenses.

Multimillion-Atom Simulations of Atomic-Level Surface Stresses and Pressure Distribution on InAs/GaAs Mesas

1999 ◽  
Vol 584 ◽  
Author(s):  
Xiaotao Su ◽  
Rajiv K. Kalia ◽  
Anupam Madhukar ◽  
Aiichiro Nakano ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Chemical Composition ◽  
Pressure Distribution ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Interatomic Potential ◽  
Atomic Level ◽  
Level Surface ◽  
Speed Up ◽  
Dynamics Simulations

AbstractLarge-scale molecular dynamics simulations are performed to investigate the atomiclevel stresses on InAs/GaAs mesas. The simulations are based on an interatomic-potential scheme for InAs/GaAs systems which depends on the local chemical composition. Multiresolution techniques are used to speed up the simulations. InAs/GaAs square mesas with { 101 }-type sidewalls are studied. The atomic-level pressure distribution and surface atomic stresses on the sidewalls with 12, 10, 8 and 6 monolayers of InAs overlayers have been calculated.

scholarly journals Enabling the execution of large scale workflows for molecular dynamics simulations

2021 ◽  
Author(s):  
Pau Andrio ◽  
Adam Hospital ◽  
Cristian Ramon-Cortes ◽  
Javier Conejero ◽  
Daniele Lezzi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Performance ◽  
Large Scale ◽  
Workflow Management ◽  
Building Blocks ◽  
Data Dependencies ◽  
Computer Scientists ◽  
Computing Platforms ◽  
Dynamics Simulations

AbstractThe usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data. On top of that, the applications typically have different parts and use different tools for each part, thus complicating the distribution and the reproducibility of the simulations. On the other hand, computer scientists concentrate on how to develop frameworks for the deployment of workflows on HPC or HTC resources; often providing separate solutions for the computational aspects and the data analytic ones.In this paper we present an approach to support biomolecular researchers in the development of complex workflows that i) allow them to compose pipelines of individual simulations built from different tools and interconnected by data dependencies, ii) run them seamlessly on different computational platforms, and iii) scale them up to the large number of cores provided by modern supercomputing infrastructures. Our approach is based on the orchestration of computational building blocks for Molecular Dynamics simulations through an efficient workflow management system that has already been adopted in many scientific fields to run applications on multitudes of computing backends.Results demonstrate the validity of the proposed solution through the execution of massively parallel runs in a supercomputer facility.

scholarly journals Development of a New Sr-O Parameterization to Describe the Influence of SrO on Iron-Phosphate Glass Structural Properties Using Molecular Dynamics Simulations

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4326
Author(s):  
Pawel Goj ◽  
Aleksandra Wajda ◽  
Pawel Stoch
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interatomic Potential ◽  
Glass Structure ◽  
Ion Pairs ◽  
Glass Network ◽  
Iron Phosphate ◽  
Phosphate Glasses ◽  
Potential Applications ◽  
Dynamics Simulations

Iron-phosphate glasses, due to their properties, have many potential applications. One of the most promising seems to be nuclear waste immobilization. Radioactive 90Sr isotope is the main short-lived product of fission and, due to its high solubility, it can enter groundwater and pose a threat to the environment. On the other hand, Sr is an important element in hard tissue metabolic processes, and phosphate glasses containing Sr are considered bioactive. This study investigated the effect of SrO addition on a glass structure of nominal 30Fe2O3-70P2O5 chemical composition using classical molecular dynamics simulations. To describe the interaction between Sr-O ion pairs, new interatomic potential parameters of the Buckingham-type were developed and tested for crystalline compounds. The short-range structure of the simulated glasses is presented and is in agreement with previous experimental and theoretical studies. The simulations showed that an increase in SrO content in the glass led to phosphate network depolymerization. Analysis demonstrated that the non-network oxygen did not take part in the phosphate network depolymerization. Furthermore, strontium aggregation in the glass structure was observed to lead to the non-homogeneity of the glass network. It was demonstrated that Sr ions prefer to locate near to Fe(II), which may induce crystallization of strontium phosphates with divalent iron.

scholarly journals Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

2016 ◽  
Vol 34 (4) ◽  
pp. 041509 ◽  
Author(s):  
Daniel Edström ◽  
Davide G. Sangiovanni ◽  
Lars Hultman ◽  
Ivan Petrov ◽  
J. E. Greene ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Epitaxial Film ◽  
Film Growth ◽  
Dynamics Simulations ◽  
Epitaxial Film Growth

scholarly journals Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

2018 ◽  
Vol 115 (45) ◽  
pp. 11519-11524 ◽  
Author(s):  
Caitlin M. Quinn ◽  
Mingzhang Wang ◽  
Matthew P. Fritz ◽  
Brent Runge ◽  
Jinwoo Ahn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Building Blocks ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Capsid Assembly ◽  
Dynamic Regulation ◽  
Angle Spinning ◽  
Dynamics Simulations ◽  
Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

scholarly journals Bimodal Grain-Size Scaling of Thermal Transport in Polycrystalline Graphene from Large-Scale Molecular Dynamics Simulations

Nano Letters ◽  
2017 ◽  
Vol 17 (10) ◽  
pp. 5919-5924 ◽  
Author(s):  
Zheyong Fan ◽  
Petri Hirvonen ◽  
Luiz Felipe C. Pereira ◽  
Mikko M. Ervasti ◽  
Ken R. Elder ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Grain Size ◽  
Molecular Dynamics Simulations ◽  
Thermal Transport ◽  
Large Scale ◽  
Size Scaling ◽  
Dynamics Simulations ◽  
Bimodal Grain Size
Sign in / Sign up

Export Citation Format

Share Document