Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer

Coarse-graining of complex networks is one of the important algorithms to study large-scale networks, which is committed to reducing the size of networks while preserving some topological information or dynamic properties of the original networks. Spectral coarse-graining (SCG) is one of the typical coarse-graining algorithms, which can keep the synchronization ability of the original network well. However, the calculation of SCG is large, which limits its real-world applications. And it is difficult to accurately control the scale of the coarse-grained network. In this paper, a new SCG algorithm based on K-means clustering (KCSCG) is proposed, which cannot only reduce the amount of calculation, but also accurately control the size of coarse-grained network. At the same time, KCSCG algorithm has better effect in keeping the network synchronization ability than SCG algorithm. A large number of numerical simulations and Kuramoto-model example on several typical networks verify the feasibility and effectiveness of the proposed algorithm.

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Energy renormalization for coarse-graining polymers having different segmental structures

Science Advances ◽

10.1126/sciadv.aav4683 ◽

2019 ◽

Vol 5 (4) ◽

pp. eaav4683 ◽

Cited By ~ 22

Author(s):

Wenjie Xia ◽

Nitin K. Hansoge ◽

Wen-Sheng Xu ◽

Frederick R. Phelan ◽

Sinan Keten ◽

...

Keyword(s):

Dynamic Properties ◽

Interaction Strength ◽

Configurational Entropy ◽

Coarse Graining ◽

Soft Materials ◽

Polymer Materials ◽

Coarse Grained ◽

Art Form ◽

Polymer Models ◽

Energy Renormalization

Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy sc in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to sc are preserved. We test this ER method by applying it to coarse-graining polymer melts (i.e., polybutadiene, polystyrene, and polycarbonate), representing polymer materials having a relatively low, intermediate, and high degree of glass “fragility”. We find that the ER method allows the dynamics of the atomistic polymer models to be faithfully described to a good approximation by CG models over a wide temperature range.

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Extraction algorithm for optimal coarse-grained networks on complex networks

International Journal of Modern Physics C ◽

10.1142/s0129183119500815 ◽

2019 ◽

Vol 30 (11) ◽

pp. 1950081

Author(s):

Lang Zeng ◽

Zhen Jia ◽

Yingying Wang

Keyword(s):

Complex Networks ◽

Network Science ◽

Dynamic Properties ◽

Coarse Graining ◽

Kuramoto Model ◽

Coarse Grained ◽

Urgent Problem ◽

Original Network ◽

Topological Information ◽

Extraction Algorithm

Coarse-graining of complex networks is a hot topic in network science. Coarse-grained networks are required to preserve the topological information or dynamic properties of the original network. Some effective coarse-graining methods have been proposed, while an urgent problem is how to obtain coarse-grained network with optimal scale. In this paper, we propose an extraction algorithm (EA) for optimal coarse-grained networks. Numerical simulation for EA on four kinds of networks and performing Kuramoto model on optimal coarse-grained networks, we find our algorithm can effectively obtain the optimal coarse-grained network.

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Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism

Soft Matter ◽

10.1039/c9sm01211g ◽

2019 ◽

Vol 15 (38) ◽

pp. 7567-7582 ◽

Cited By ~ 3

Author(s):

Shu Wang ◽

Zhen Li ◽

Wenxiao Pan

Keyword(s):

Polymer Solutions ◽

Dynamic Properties ◽

Coarse Graining ◽

Coarse Grained ◽

Implicit Solvent ◽

Bottom Up ◽

System P

We present a bottom-up coarse-graining (CG) method to establish implicit-solvent CG modeling for polymers in solution, which conserves the dynamic properties of the reference microscopic system.

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Transfer learning of memory kernels for transferable coarse-graining of polymer dynamics

Soft Matter ◽

10.1039/d1sm00364j ◽

2021 ◽

Author(s):

Zhan Ma ◽

Shu Wang ◽

Minhee Kim ◽

Kaibo Liu ◽

Chun-Long Chen ◽

...

Keyword(s):

Transfer Learning ◽

Dynamic Properties ◽

Coarse Graining ◽

Polymer Dynamics ◽

Coarse Grained ◽

Atomistic Systems

The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on...

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The distribution of antigen on the surface of RBL-2H3 rat basophilic leukemia cells observed by back-scattered electron imaging

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100142992 ◽

1986 ◽

Vol 44 ◽

pp. 274-275

Author(s):

R.F. Stump ◽

J.R. Pfeiffer ◽

JC. Seagrave ◽

D. Huskisson ◽

J.M. Oliver

Keyword(s):

Cell Surface ◽

Dynamic Properties ◽

Leukemia Cells ◽

Antigen Binding ◽

Scattered Electron ◽

Ige Receptor ◽

Receptor Complexes ◽

Rat Basophilic Leukemia Cells ◽

Electron Imaging ◽

Basophilic Leukemia

In RBL-2H3 rat basophilic leukemia cells, antigen binding to cell surface IgE-receptor complexes stimulates the release of inflammatory mediators and initiates a series of membrane and cytoskeletal events including a transformation of the cell surface from a microvillous to a lamellar topography. It is likely that dynamic properties of the IgE receptor contribute to the activation of these responses. Fewtrell and Metzger have established that limited crosslinking of IgE-receptor complexes is essential to trigger secretion. In addition, Baird and colleagues have reported that antigen binding causes a rapid immobilization of IgE-receptor complexes, and we have demonstrated an apparent increase with time in the affinity of IgE-receptor complexes for antigen.

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Nucleosome dynamics

Biochemical Society Symposium ◽

10.1042/bss0730109 ◽

2006 ◽

Vol 73 ◽

pp. 109-119 ◽

Cited By ~ 2

Author(s):

Chris Stockdale ◽

Michael Bruno ◽

Helder Ferreira ◽

Elisa Garcia-Wilson ◽

Nicola Wiechens ◽

...

Keyword(s):

High Resolution ◽

Chromatin Structure ◽

Current Knowledge ◽

Dynamic Properties ◽

Structure And Dynamics ◽

Nucleosome Dynamics ◽

Sharp Focus ◽

Recent Advances ◽

Insight Into ◽

Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

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