Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations

2018 ◽  
Vol 149 (24) ◽  
pp. 244114 ◽  
Author(s):  
Gregor Deichmann ◽  
Nico F. A. van der Vegt
Keyword(s):  
Dynamic Properties ◽  
Molecular Simulations ◽  
Coarse Grained ◽  
Bottom Up

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

Soft Matter ◽  
2019 ◽  
Vol 15 (38) ◽  
pp. 7567-7582 ◽  
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.

Bottom-up derived flexible water model with dipole and quadrupole moments for coarse-grained molecular simulations

2020 ◽  
Vol 22 (46) ◽  
pp. 27394-27412
Author(s):  
Chen Li ◽  
Zhongyuan Qin ◽  
Wei Han
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained ◽  
Water Model ◽  
Quadrupole Moments ◽  
Bottom Up ◽  
Structural Correlation

A bottom-up CG water model is developed to capture the electrostatic multipoles, structural correlation and thermodynamics of water.

scholarly journals Introducing Memory in Coarse-Grained Molecular Simulations

2021 ◽  
Author(s):  
Viktor Klippenstein ◽  
Madhusmita Tripathy ◽  
Gerhard Jung ◽  
Friederike Schmid ◽  
Nico F. A. van der Vegt
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

A new spectral coarse-graining algorithm based on K-means clustering in complex networks

2019 ◽  
Vol 33 (01) ◽  
pp. 1850421 ◽  
Author(s):  
Lang Zeng ◽  
Zhen Jia ◽  
Yingying Wang
Keyword(s):  
Complex Networks ◽  
Large Scale ◽  
Dynamic Properties ◽  
Coarse Graining ◽  
Kuramoto Model ◽  
Coarse Grained ◽  
Original Network ◽  
Topological Information ◽  
Real World Applications ◽  
Large Scale Networks

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.

scholarly journals Low-amplitude dynamic tests of fine gravel in a resonant column

2019 ◽  
Vol 97 ◽  
pp. 04024
Author(s):  
Zaven Ter-Martirosyan ◽  
Evgeny Sobolev ◽  
George Anzhelo
Keyword(s):  
Mechanical Properties ◽  
Dynamic Properties ◽  
Sample Volume ◽  
Coarse Grained ◽  
Software Systems ◽  
Resonant Column ◽  
Dynamic Effects ◽  
Laboratory Equipment ◽  
Aggregate Fractions ◽  
Sample Assembly

Construction of industrial and civil buildings, taking into account the dynamic effects on the foundations, requires special experiments on the mechanical properties of soils. This article presents the results of studying the dynamic properties of coarse gravelly soils using the resonant column method. These studies are relevant, since the determination of the dynamic properties of coarse-grained soils under laboratory conditions is associated with a restriction on the size of the fractions in the sample volume. This circumstance leads to the fact that at the moment most of the laboratory tests of the dynamic properties of coarse-grained soils are performed on smaller aggregate fractions, which, in general, significantly reduces the resulting mechanical properties of soils. It does not reflect the real operation of the foundation of buildings during dynamic effects. This paper presents a description of the available laboratory equipment, the sequence of preparation of samples of coarse grained crushed stone soil and sample assembly in the working chamber of the installation. The article contains the main graphs characterizing the change in shear modulus and damping coefficient depending on shear deformations. It is noted that the results obtained are particularly relevant for modeling the dynamic effects of natural and man-made character on the foundations of industrial and civil buildings, the bases of which are composed of coarse-grained soils. Dynamic parameters considered in this paper, can and must be used in numerical calculations by finite element method with the use of modern groundwater models in geotechnical software systems.

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