Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back

ChemPhysChem ◽  
2002 ◽  
Vol 3 (9) ◽  
pp. 754-769 ◽  
Author(s):  
Florian Müller-Plathe
Soft Matter ◽  
2015 ◽  
Vol 11 (38) ◽  
pp. 7639-7647 ◽  
Author(s):  
Francesco Puosi ◽  
Julien Olivier ◽  
Kirsten Martens

Coarse-graining flow dynamics of amorphous systems: mesoscopic scale stress fluctuations are created by the elastic response to surrounding yielding events.


2021 ◽  
Vol 103 (1) ◽  
Author(s):  
Leonardo R. Cadorim ◽  
Antonio R. de C. Romaguera ◽  
Isaías G. de Oliveira ◽  
Rodolpho R. Gomes ◽  
Mauro M. Doria ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daiji Ichishima ◽  
Yuya Matsumura

AbstractLarge scale computation by molecular dynamics (MD) method is often challenging or even impractical due to its computational cost, in spite of its wide applications in a variety of fields. Although the recent advancement in parallel computing and introduction of coarse-graining methods have enabled large scale calculations, macroscopic analyses are still not realizable. Here, we present renormalized molecular dynamics (RMD), a renormalization group of MD in thermal equilibrium derived by using the Migdal–Kadanoff approximation. The RMD method improves the computational efficiency drastically while retaining the advantage of MD. The computational efficiency is improved by a factor of $$2^{n(D+1)}$$ 2 n ( D + 1 ) over conventional MD where D is the spatial dimension and n is the number of applied renormalization transforms. We verify RMD by conducting two simulations; melting of an aluminum slab and collision of aluminum spheres. Both problems show that the expectation values of physical quantities are in good agreement after the renormalization, whereas the consumption time is reduced as expected. To observe behavior of RMD near the critical point, the critical exponent of the Lennard-Jones potential is extracted by calculating specific heat on the mesoscale. The critical exponent is obtained as $$\nu =0.63\pm 0.01$$ ν = 0.63 ± 0.01 . In addition, the renormalization group of dissipative particle dynamics (DPD) is derived. Renormalized DPD is equivalent to RMD in isothermal systems under the condition such that Deborah number $$De\ll 1$$ D e ≪ 1 .


Nano Letters ◽  
2021 ◽  
Author(s):  
Alberto Trentino ◽  
Jacob Madsen ◽  
Andreas Mittelberger ◽  
Clemens Mangler ◽  
Toma Susi ◽  
...  

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 659
Author(s):  
Jue Lu ◽  
Ze Wang

Entropy indicates irregularity or randomness of a dynamic system. Over the decades, entropy calculated at different scales of the system through subsampling or coarse graining has been used as a surrogate measure of system complexity. One popular multi-scale entropy analysis is the multi-scale sample entropy (MSE), which calculates entropy through the sample entropy (SampEn) formula at each time scale. SampEn is defined by the “logarithmic likelihood” that a small section (within a window of a length m) of the data “matches” with other sections will still “match” the others if the section window length increases by one. “Match” is defined by a threshold of r times standard deviation of the entire time series. A problem of current MSE algorithm is that SampEn calculations at different scales are based on the same matching threshold defined by the original time series but data standard deviation actually changes with the subsampling scales. Using a fixed threshold will automatically introduce systematic bias to the calculation results. The purpose of this paper is to mathematically present this systematic bias and to provide methods for correcting it. Our work will help the large MSE user community avoiding introducing the bias to their multi-scale SampEn calculation results.


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