A MULTI-SCALE NONEQUILIBRIUM MOLECULAR DYNAMICS ALGORITHM AND ITS APPLICATIONS

2009 ◽  
Vol 01 (03) ◽  
pp. 405-420 ◽  
Author(s):  
NI SHENG ◽  
SHAOFAN LI
Keyword(s):  
Molecular Dynamics ◽  
Local Equilibrium ◽  
Random Force ◽  
Coarse Grained ◽  
Nonequilibrium Molecular Dynamics ◽  
Fine Scale ◽  
Coarse Scale ◽  
Fe Method ◽  
Time Step ◽  
Multi Scale

In this paper, we introduce a multi-scale nonequilibrium molecular dynamics (MS-NEMD) model that is capable of simulating nano-scale thermal–mechanical interactions. Recent simulation results using the MS-NEMD model are presented. The MS-NEMD simulation generalises the nonequilibrium molecular dynamics (NEMD) simulation to the setting of concurrent multi-scale simulation. This multi-scale framework is based on a novel concept of multi-scale canonical ensemble. Under this concept, each coarse scale finite element (FE) node acts as a thermostat, while the atoms associated with each node are assumed to be in a local equilibrium state within one coarse scale time step. The coarse scale mean field is solved by the FE method based on a coarse-grained thermodynamics model; whereas in the fine scale the NEMD simulation is driven by the random force that is regulated by the inhomogeneous continuum filed through a distributed Nośe–Hoover thermostat network. It is shown that the fine scale distribution function is canonical in the sense that it obeys a drifted local Boltzmann distribution.

Multibody Molecular Dynamics I: Theoretical Development

2007 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Kurt S. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Multibody Dynamics ◽  
Temporal Integration ◽  
Interaction Force ◽  
Theoretical Development ◽  
Coarse Grained ◽  
Unified Framework ◽  
Multi Scale ◽  
Integration Schemes ◽  
Dynamics Simulations

This is the first paper in a series of two papers on using multibody dynamics algorithms and methods for coarse-grained molecular dynamics simulations. This paper presents the underlying framework for multi-scale modelling of biomolecules and polymers. In this framework, the system to be simulated is sub-structured into a hierarchy of multi-resolution models that are simulated using efficient multibody dynamics algorithms. The algorithms work in a unified framework, enabling efficient multi-scale (or multi-resolution) simulations. A discussion of the hierarchy of models with different resolutions along with the salient features of the appropriate multibody dynamics algorithms used for simulating them is presented. The unified scheme and the qualitative advantages of the method are discussed. Important implementation details such as boundary conditions, temporal integration schemes, interaction force field calculations and solvent models are also presented. In the next paper applications and results are discussed.

AN APPROACH TO DATA PARALLEL MOLECULAR DYNAMICS FOR LIQUIDS

1993 ◽  
Vol 04 (01) ◽  
pp. 41-48 ◽  
Author(s):  
FREDRIK HEDMAN ◽  
AATTO LAAKSONEN
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Nearest Neighbor ◽  
Large Fraction ◽  
Particle Migration ◽  
Coarse Grained ◽  
Time Step ◽  
Data Parallel ◽  
Massively Parallel Computers ◽  
Large Scale Data

An efficient approach to large scale data parallel short-range molecular dynamics for liquids is presented. The method is based on the coarse-grained cell method in which the simulation cell is decomposed into equally sized subcells, with the shortest side being larger than the cut-off radius. To avoid a large fraction of the nonproductive calculations we develop a geometric sorting procedure based on particle distances to subcell boundaries. Due to particle migration, the contents of the subcells need to be updated. This is done with a method based only on nearest-neighbor communications. Special "null-particles" are introduced, which act as buffers during periodic updates and allow for a globally uniform algorithm during the force calculations. The method should be easy to implement on most massively parallel computers of SIMD or MIMD type. We have implemented our code in CM Fortran on an 8K CM200. Communication cost is around 7% of the total cpu time. The overall speed for one million particles is approximately 5.9μs per MD time step and per particle and 5.5μs for five million particles.

Rheological and Structural Properties of Associated Polymer Networks Studied via Nonequilibrium Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Yuankun Peng ◽  
Tongkui Yue ◽  
Sai Li ◽  
Ke Gao ◽  
Yachen Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Properties ◽  
Functional Groups ◽  
Molecular Level ◽  
Polymer Networks ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Nonequilibrium Molecular Dynamics ◽  
Nonequilibrium Molecular Dynamics Simulation

An intensive understanding of the rheological and structural properties of polymer physical networks formed via the associative functional groups at the molecular level is still lacking. Herein, we employed coarse-grained...

Simultaneous uniaxial extensional deformation and cylindrical confinement of block copolymers using non-equilibrium molecular dynamics

Soft Matter ◽  
2018 ◽  
Vol 14 (8) ◽  
pp. 1389-1396 ◽  
Author(s):  
George L. Shebert ◽  
Yong Lak Joo
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymers ◽  
Coarse Grained ◽  
Nonequilibrium Molecular Dynamics ◽  
Combined Effects ◽  
Extensional Deformation ◽  
Non Equilibrium Molecular Dynamics ◽  
Symmetric Block ◽  
Non Equilibrium

Using coarse-grained nonequilibrium molecular dynamics, symmetric block copolymers are simulated under the combined effects of cylindrical confinement and uniaxial extensional deformation.

Image Segmentation Based on Contextual Label Tree for Retrieval

2010 ◽  
Vol 121-122 ◽  
pp. 563-568
Author(s):  
Guo Qiang Yuan ◽  
He Shan Liu
Keyword(s):  
Image Segmentation ◽  
Hidden Markov ◽  
Fine Scale ◽  
Wavelet Domain ◽  
Segmentation Method ◽  
Coarse Scale ◽  
Label Tree ◽  
Multi Scale ◽  
Tree Node ◽  
Important Constituent

Image segmentation is an important constituent portion in image processing and retrieval. Based on the traditional Wavelet-domain Hidden Markov Tree (HMT) Multi-scale Segmentation method, this paper presents a Contextual Label Tree (CLT) method according to the dependency information between image blocks belong to different scales, including the relation from the father node, the neighbor nodes and the neighbor nodes of the father. This method calculates the maximal similarity using context vectors that exit on every tree node and realizes image segmentation from coarse-scale to fine-scale. Experiments show that this method is satisfied with its segmentation performance.

scholarly journals Interfacial Interaction Enhanced Rheological Behavior in PAM/CTAC/Salt Aqueous Solution—A Coarse-Grained Molecular Dynamics Study

Polymers ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 265 ◽  
Author(s):  
Dongjie Liu ◽  
Yong Li ◽  
Fei Liu ◽  
Wenjing Zhou ◽  
Ansu Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Shear Viscosity ◽  
Chemical Engineering ◽  
Surfactant Solution ◽  
Coarse Grained ◽  
Nonequilibrium Molecular Dynamics ◽  
Mixed Solution ◽  
Surfactant Mixtures ◽  
Processing Control ◽  
Polymer Surfactant

Interfacial interactions within a multi-phase polymer solution play critical roles in processing control and mass transportation in chemical engineering. However, the understandings of these roles remain unexplored due to the complexity of the system. In this study, we used an efficient analytical method—a nonequilibrium molecular dynamics (NEMD) simulation—to unveil the molecular interactions and rheology of a multiphase solution containing cetyltrimethyl ammonium chloride (CTAC), polyacrylamide (PAM), and sodium salicylate (NaSal). The associated macroscopic rheological characteristics and shear viscosity of the polymer/surfactant solution were investigated, where the computational results agreed well with the experimental data. The relation between the characteristic time and shear rate was consistent with the power law. By simulating the shear viscosity of the polymer/surfactant solution, we found that the phase transition of micelles within the mixture led to a non-monotonic increase in the viscosity of the mixed solution with the increase in concentration of CTAC or PAM. We expect this optimized molecular dynamic approach to advance the current understanding on chemical–physical interactions within polymer/surfactant mixtures at the molecular level and enable emerging engineering solutions.

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