Reverse Mapping of Coarse-Grained Polyethylene Chains from the Second Nearest Neighbor Diamond Lattice to an Atomistic Model in Continuous Space

1997 ◽  
Vol 30 (18) ◽  
pp. 5520-5526 ◽  
Author(s):  
Pemra Doruker ◽  
Wayne L. Mattice
Keyword(s):  
Nearest Neighbor ◽  
Diamond Lattice ◽  
Coarse Grained ◽  
Atomistic Model ◽  
Continuous Space ◽  
Reverse Mapping

scholarly journals Fault Diagnosis Method for Rolling Bearings Based on Composite Multiscale Fluctuation Dispersion Entropy

Entropy ◽  
2019 ◽  
Vol 21 (3) ◽  
pp. 290 ◽  
Author(s):  
Xiong Gan ◽  
Hong Lu ◽  
Guangyou Yang
Keyword(s):  
Fault Diagnosis ◽  
Nearest Neighbor ◽  
Coarse Grained ◽  
K Nearest Neighbor ◽  
Rolling Bearings ◽  
Entropy Estimation ◽  
Fault Recognition ◽  
Knn Classifier ◽  
Diagnosis Method ◽  
The Stability

This paper proposes a new method named composite multiscale fluctuation dispersion entropy (CMFDE), which measures the complexity of time series under different scale factors and synthesizes the information of multiple coarse-grained sequences. A simulation validates that CMFDE could improve the stability of entropy estimation. Meanwhile, a fault recognition method for rolling bearings based on CMFDE, the minimum redundancy maximum relevancy (mRMR) method, and the k nearest neighbor (kNN) classifier (CMFDE-mRMR-kNN) is developed. For the CMFDE-mRMR-kNN method, the CMFDE method is introduced to extract the fault characteristics of the rolling bearings. Then, the sensitive features are obtained by utilizing the mRMR method. Finally, the kNN classifier is used to recognize the different conditions of the rolling bearings. The effectiveness of the proposed CMFDE-mRMR-kNN method is verified by analyzing the standard experimental dataset. The experimental results show that the proposed fault diagnosis method can effectively classify the conditions of rolling bearings.

scholarly journals Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment

2011 ◽  
Vol 78 (3) ◽  
pp. 759-767 ◽  
Author(s):  
Xueju Lin ◽  
David Kennedy ◽  
Aaron Peacock ◽  
James McKinley ◽  
Charles T. Resch ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Nearest Neighbor ◽  
Sequence Similarity ◽  
Anaerobic Respiration ◽  
16S Rrna Genes ◽  
Coarse Grained ◽  
Rrna Genes ◽  
Achromobacter Xylosoxidans ◽  
Hanford Site ◽  
Content Type

ABSTRACTSubsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. ThenosZgene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. MostnosZsequences were affiliated withOchrobactrum anthropi(97 sequence similarity) or had a nearest neighbor ofAchromobacter xylosoxidans(90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of thedsrAgene andGeobacteraceaehad the highest relative abundance. The majority ofdsrAgenes detected near the interface were related toDesulfotomaculumspp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.

A Simple Reverse Mapping Procedure for Coarse-Grained Polymer Models with Rigid Side Groups

2011 ◽  
Vol 44 (13) ◽  
pp. 5520-5526 ◽  
Author(s):  
Azadeh Ghanbari ◽  
Michael C. Böhm ◽  
Florian Müller-Plathe
Keyword(s):  
Coarse Grained ◽  
Mapping Procedure ◽  
Polymer Models ◽  
Reverse Mapping

A COARSE-GRAINED MODEL OF MONOOLEIN: COMPARISON WITH THE ATOMISTIC MODEL

2009 ◽  
Vol 08 (01n02) ◽  
pp. 169-173
Author(s):  
J. H. KIM ◽  
S. H. CHOI ◽  
D. H. JUNG ◽  
C. S. CHO ◽  
Y. J. CHOI
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayer ◽  
Dissipative Particle Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Model ◽  
Coarse Grained Model ◽  
Cosmetic Industry ◽  
Dynamics Simulations ◽  
Potential Parameters

Monoolein (2,3-dihydroxypropyl (Z)-octadec-9-enoate) is one of the monoacylglycerol and has been studied for various applications in food, pharmaceutical, and cosmetic industry. Those applications make use of the phase behavior of monoolein. In order to understand the lipid bilayer phase of monoolein in mesoscale, a coarse-grained model has been built and tested in this work. The monoolein molecule was represented by two hydrophilic heads and six hydrophobic tails. The three water molecules were also represented as one bead. For comparison, the atomistic model has also been used for molecular dynamics simulation on the lipid bilayer phase in isothermal-isobaric (NPT) ensemble. The interaction and bond bending potential parameters for dissipative particle dynamics (DPD) were obtained with molecular dynamics simulations on lipid bilayer in water. And we also obtained the interaction parameters of the coarse-grained model, which agree well with the atomistic model. We compared the simulated phases using the coarse-grained model with using the atomistic model. With these parameters, we successfully reproduced the lamella phase of monoolein in DPD simulations.

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.

Hybrid coarse-grained/atomistic model of “chitosan + carbon nanostructures” composites

2014 ◽  
Vol 20 (10) ◽  
Author(s):  
Elena L. Kossovich ◽  
Irina V. Kirillova ◽  
Leonid Yu. Kossovich ◽  
Roman A. Safonov ◽  
Dmitriy V. Ukrainskiy ◽  
...  
Keyword(s):  
Carbon Nanostructures ◽  
Coarse Grained ◽  
Atomistic Model

Molecular Dynamics Simulation of the Glass Transition of Ortho-Terphenyl in Bulk and Thin Films

2006 ◽  
Vol 924 ◽  
Author(s):  
Jayeeta Ghosh ◽  
Roland Faller
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
A Priori ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Technological Advancement ◽  
Atomistic Model ◽  
Reorientation Dynamics ◽  
Bulk Model ◽  
Dynamics Simulations

ABSTRACTThe glass transition temperature in thin film depends strongly on film thickness and interaction with the substrate and it is normally a priori not clear which way it deviates from the bulk value. This causes new challenge in the technological advancement of smaller and smaller electronic devices. In this study molecular dynamics simulations of a low-molecular weight organic glass former, ortho-terphenyl, are carried out in bulk and freestanding films. The main motivation is to provide insight into the confinement effect without interface interactions. Based on earlier models of ortho-terphenyl we developed an atomistic model for bulk simulations. The model reproduces the literature data from simulations as well as experiments. After characterizing the bulk model we form a freestanding film. This film gives us the opportunity to study the dynamical heterogeneity near the glass transition by in-plane mobility and reorientation dynamics. We also develop a structurally coarse-grained model for this glass former based on our atomistic model to study bigger system for a longer period of time.

scholarly journals An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids

2018 ◽  
Author(s):  
Emanuele Locatelli ◽  
Lorenzo Rovigatti
Keyword(s):  
Phase Diagram ◽  
Free Energy ◽  
Large Scale ◽  
Nearest Neighbor ◽  
Numerical Study ◽  
Thermodynamic Description ◽  
Numerical Approach ◽  
Quantitative Agreement ◽  
State Theory ◽  
Coarse Grained

We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest order virial expansion and a nearest-neighbor DNA model, can provide, in an undemanding way, a thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of such scheme are as accurate as the ones obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.

Coarse-grained modeling of cell division in 3D: influence of density, medium viscosity, and inter-membrane friction on cell growth and nearest neighbor distribution

2020 ◽  
Vol 18 (2-3) ◽  
pp. 150-162
Author(s):  
Pranav Madhikar ◽  
Jan Åström ◽  
Jan Westerholm ◽  
Björn Baumeier ◽  
Mikko Karttunen
Keyword(s):  
Cell Division ◽  
Cell Growth ◽  
Nearest Neighbor ◽  
Coarse Grained ◽  
Medium Viscosity
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